A two-dimensional code file reorganization method and system are operated in a file reorganization system and comprise the following steps that the reorganization system inputs files to be reorganizedto an archiving module, recorded files with two-dimensional codes are generated, and the recorded files are printed; wherein the two-dimensional code comprises a digital address, a parcel number, a file number or a shelf number, the two-dimensional code is scanned on the paper recorded file after the paper recorded file is manually shelved, the shelved file is compared, and comparison informationis sent. According to the method, the problem that online and offline archives of an original traditional archive system cannot be automatically associated is solved, online and offline archive association is achieved by introducing the two-dimensional code, the position of the electronic archive is automatically positioned through the code scanning gun and the system, and the working efficiencyof an archive administrator is improved.