A system is provided to facilitate tag-based organization of documents. During operation, the system receives an original user query. The system extends the query to include documents with an IN-tag and exclude documents with an OUT-tag. The system then performs a search based on the extended query to indicate a collection of documents which satisfy the extended query. The system further allows a user to add a document to the collection of documents or remove a document from the collection of documents. Next, the system modifies a tagging property of the document.