A portable storage device capable of automatically running biometrics application programs includes a control module, a storage unit and a biometrics sensor. The control module, in which firmware is stored, is electrically connected to a terminal host, a storage unit and a biometrics sensor. The firmware is configured to divide the storage unit into a plurality of blocks including a biometrics application program block and a private block. The biometrics application program block stores at least one biometrics application program. The firmware enables an operation system of the terminal host to treat the biometrics application program block as an compact disk drive and disables or closes the compact disk drive after automatic running the at least one biometrics application program. The least one biometrics application program guides a user to perform a biometrics identification procedure, and then enables a specific operation.