The invention discloses a mobile data application safety protection system and a mobile data application safety protection method based on a USBKey. The USBKey is distributed through an intranet data safety managing device, a mobile data file needing to be carried is stored in a hidden partition of the USBKey, identity authentication is carried out on a user through the identity authentication information in a read-only partition of USBKey data, safety control is carried out on the using behavior of the mobile data file by operating a drive control program in a starting-partition, a safety audit is carried out on the whole using process, and after being used, the USBKey needs to be logged out and recycled to be distributed for the next time. Data information leakage caused by data recovery when the USBKey is lost or taken out for being maintained can be prevented through the identity authentication and the data file transparent encryption and decryption; the occurrence that data files in the USBKey are copied or saved as another files by the user and data information is stored in other media can be prevented through a system message hook and a disk control program.