A portable encrypted storage device with biometric identification includes a host interface connected to a terminal host, a controller connected to the host interface, a memory module, a fingerprint sensor, an encryption/decryption chip and a portable large-capacity storage unit connected to the controller. The controller communicates with the host by handshakes and enables the host to automatically run a fingerprint identification driver and application program from the memory module to the host. The host receives an instruction from the user through the driver and program, and informs the controller to control the fingerprint sensor to read to-be-recognized fingerprint data of the user. The host judges whether or not the to-be-recognized fingerprint data substantially matches with a fingerprint template stored in the memory module. If a match occurs, the host can recognize and access the hidden portable large-capacity storage unit through the encryption/decryption chip.