Flexnote vs SiYuan: Linked Documents and an Infinite Canvas for Research

SiYuan and Flexnote both store notes on the user’s device. Opening a library does not require an account that must stay online. Both are local-first. The main difference is the working surface.

SiYuan works in documents. Content is stored as blocks and can reference other blocks. A single document can run very long, and the graph view is there to revisit links. Flexnote works on an infinite canvas. Each excerpt or judgment is its own card, and a card’s position stands for a relationship that is not yet written out. When papers, slides, and lecture recordings do not yet have an order, they can sit next to the related material before a section title is chosen.

When evaluating a SiYuan alternative, name the capability that needs replacing. If the requirement is a bidirectional-link editor and flashcards, Flexnote does not match it. Both products include a database: SiYuan is an attribute table on documents, and Flexnote is a tag database organized around cards. If the requirement is to lay a large set of materials side by side, the differences below are the relevant ones. Prices follow the SiYuan pricing page as of 24 October 2026.

SiYuan: a document that can be cited

SiYuan is open-source personal knowledge management software under AGPL-3.0. The editor is Markdown WYSIWYG, with outline lists, block references, bidirectional links, and a graph view. The project states that a computer of ordinary specification can edit documents on the order of a million characters. Formulas, flowcharts, Gantt charts, and similar typesetting elements are built in and do not require a separate plugin.

Local core features are free, including for commercial use. The official list includes block references, custom attributes, embedded SQL queries, database table views, FSRS flashcards, PDF annotation linked back to notes, web clipping, continuation and Q&A through an OpenAI API, OCR, templates, JavaScript and CSS snippets, and the community marketplace.

Clients cover Windows, macOS, Linux, Android, iOS, and HarmonyOS. The kernel can be deployed with Docker on a server the user controls, with access limited by an authorization code. Themes, plugins, and widgets in the marketplace change the editor’s appearance and workflow.

A whiteboard is not SiYuan’s main surface. The community provides an Excalidraw widget. Once embedded, it can fill a document and reference blocks in the library. The container is still that document. The whiteboard exists as a widget.

Flexnote: a canvas for material that is not yet prose

Flexnote’s unit of notes is the card. One card holds one excerpt, claim, or judgment. Cards connect through bidirectional links and tags. Search happens in the card library: the canvas shows relationships that do not yet have names, and the library retrieves cards by tag and whiteboard. The daily note collects that day’s loose records.

The canvas uses Flexnote’s own renderer, aimed at panning and zooming with hundreds to thousands of cards. A document editor places body text in a scrolling region and does not deal with a count of cards on a plane. When one topic stays on one canvas for a long time, smoothness affects daily use before the feature list does.

The same card can sit on more than one whiteboard. When a topic is split into “literature,” “concepts,” and “to write,” the excerpt does not need to be copied. As the number of whiteboards grows, the card library remains one set of cards.

PDF annotation and video annotation

SiYuan includes PDF reading and annotation, and annotations can link both ways to blocks. When notes still live in documents and the material is mostly paper PDFs, that path is complete. Feedback in the official repository clusters on two points: text inside a PDF cannot be edited directly, and a highlight has to be copied into the body before it becomes a note that can be typeset. The reader is connected to blocks. An excerpt does not automatically become a card that can move to another topic.

Flexnote annotates cards, PDFs, local video, online course video such as YouTube, and audio. Highlights and timestamps stay on the source and link back to the canvas. A lecture recording or podcast does not require a separate player, and subtitles do not have to be pasted into a document first.

SiYuan has no equivalent built-in video annotation. A third-party browser extension can send Bilibili and YouTube content into notes. It is aimed mainly at the web app, and templates and an API token have to be configured by the user. The path works, and it requires extra setup.

What SiYuan has and Flexnote does not

The following capabilities directly affect whether to stay with SiYuan. Flexnote does not provide them.

• Flashcards. SiYuan uses FSRS for spaced repetition. Flexnote has no review queue and no memory algorithm.
• Long-form export and publishing. SiYuan can copy content to WeChat Official Accounts, Zhihu, and Yuque, and export PDF, Word, and HTML. Flexnote’s usual export is a whiteboard, or a whiteboard exported as PDF, rather than a typeset article for WeChat.
• Open source and self-hosting. SiYuan is AGPL-3.0 and provides a marketplace, snippets, an HTTP API, and Docker. Flexnote has no equivalent plugin marketplace, and the source is not open. If the implementation must be audited, or the note service must run on a machine the user controls, SiYuan already provides that.

Databases: attribute views and a tag database

SiYuan’s database is an attribute view. Blocks can carry custom attributes and be shown as a table. Databases can relate to one another and roll values up. Filtering documents by field and keeping a project ledger are a complete path.

Flexnote’s database is a tag database. Cards of one kind share a tag and can then be viewed under that tag as a list or a kanban. Properties are created by the user and can be used to filter and sort. The tag database follows cards and tags. It is not a separate multi-table relation system.

Both products include a database, and they organize different objects. SiYuan is closer to an attribute table on documents. Flexnote adds custom fields to cards on the canvas, then arranges those cards as a list or a kanban.

Local storage and the cost of sync

SiYuan keeps notes in a workspace on the local machine, and editing continues offline. Standard Markdown is the import and export format. The workspace on disk is SiYuan’s own data directory, not a folder of Markdown files that can be dropped into another editor. Export comes before a change of software.

Sync across devices is a paid capability. The project states that third-party sync disks must not be used to sync the whole workspace, because that can corrupt data. Folder sync from the Baidu Netdisk or Nutstore clients is not a supported sync method. Sync uses the interfaces SiYuan provides.

• Local features, ¥0. There is no limit on the number of notes.
• Feature pack, ¥80, one-time (¥96 on the pricing page before discount). This unlocks S3 and WebDAV sync and backup. Storage is purchased or hosted separately. WebDAV does not support Nutstore.
• Official cloud, ¥148 per year (¥192 on the pricing page before discount). This includes the feature pack, plus 8 GB of official space, official sync and backup, asset hosting, a cloud inbox, and scheduled WeChat reminders. Official sync is end-to-end encrypted. Payments are not refunded. A trial can be started in the desktop app under Settings → Account. The renewal price is locked to the first subscription. A student discount exists; the rate is the one stated on the official page.

8 GB is the official ceiling. For a larger library, the project recommends S3. That interface is included in the annual plan and can also be bought alone as the ¥80 feature pack.

Flexnote’s free plan is 100 cards, local storage, and one device, with no required sign-in. Cloud sync is part of Pro. It moves a library among the user’s own devices and does not provide simultaneous multi-user editing. Targets are Baidu Netdisk, OneDrive, S3, and WebDAV. A whiteboard can be shown to someone else through a publish link in the browser. A canvas can be exported as PDF.

If the user already has S3 or WebDAV and only needs the notes to open on a second device, SiYuan’s one-time ¥80 fee covers that. Flexnote sync is included in Pro, at ¥59 per quarter, ¥99 per year, or ¥269 as a one-time purchase. Pro also includes capacity beyond the free limit, not only sync.

The free limits differ more sharply. SiYuan does not cap the number of local notes. Flexnote’s free plan stops at 100 cards, which is not enough for a knowledge base used continuously over several years.

Feature comparison

Choose by the next piece of work

If the next job is a long document, a project ledger across related tables, or a review queue for facts to memorize, stay with SiYuan. Requirements for HarmonyOS, Docker, the marketplace, or an open-source license also do not match Flexnote. If the cards are already on a canvas and the need is to filter by custom fields or switch to a kanban, use Flexnote’s tag database.

If the next job is to place several papers, one lecture’s PDF, and a recording on the same plane, lift sentences, and move them to another topic, the Flexnote free plan is enough for one trial. One hundred cards are enough to judge whether a canvas fits that work better than a document. If it does, then weigh ¥99 per year or ¥269 once. If it does not, stop. Local editing in SiYuan is not charged.

For other local-first note apps, see local-first note-taking apps. For PDF-only annotation, see how to take notes on a PDF.