The invention provides a document secret management method and system based on digital labels, and belongs to the technical field of information security. The document secret management system classifies digital label keys and labels different digital labels on the documents according to the different security levels and use ranges of the documents; therefore, the document authorities are subdivided; the transmission and use security of the documents can be ensured; the digital labels are encryption keys; the keys are stored in encryption cards; the keys are issued by the management system and are imported in the encryption cards through a USBkey form; the keys are divided into three kinds: a local machine, a local department and a local unit; the documents are encrypted through the different keys; and the documents are protected according to levels.