The invention provides a taxation document handling self-service terminal and a running method, and belongs to the technical field of self-service operation computers. The taxation document handling self-service terminal comprises an input module, an identity verification module, a scanning module, a conveying module, a printing module, a packaging module, a storage module and a master control module, wherein the conveying module is used for conveying a target document and a business voucher to the packaging module, the printing module is used for printing the business voucher of a user according to a control signal, the packaging module is used for packaging the target document and the business voucher, and the storage module is used for storing the packaged business voucher and target document. The taxation document handling self-service terminal can convey the target document and package and store the target document meeting preset requirements; by means of the running method, the comprehensively self-service process of form filling, identity verification, document checking, document packaging, document uploading, document storing and result feedback can be achieved for a taxpayer, so that the work efficiency of the tax bureau is improved, the business handling process is simplified for the taxpayer, and full self-service and unattended business handling is achieved.