The invention discloses a method for encrypting a USB flash disk with fingerprint authentication. The USB flash disk is encrypted in a partition mode, namely the USB flash disk is divided into two drives, and a user can select one drive for use according to needs; the current up-to-date symmetric cryptographic algorithm is adopted, is higher in safety level compared with other encrypted USB flash disks and meets the current national conditions; an encryption key is canceled, a secret key is generated from fingerprints, and a file is encrypted or decrypted through the secret key generated from the fingerprints. The secret key is generated from extracted fingerprint characteristic values through a pseudo-random number generation algorithm, in this way, only the fingerprint characteristic values need to be stored, storage space needing to be occupied is reduced, information quantity is reduced, the possibility of effective information disclosure is reduced, fingerprint authentication and the encryption and decryption processes are combined, safety of an overall system is improved, the user can use the USB flash disk conveniently, and the trouble that the user forgets a common command is saved. The file encrypting operation is based on the homemade symmetric cryptographic algorithm, and the independent and controllable requirements for information safety products by China are met.