A storage device protection system including a protection control unit, a detection unit, an account/password input unit, an ID acquiring unit, and an encryption unit is provided. The detection unit determines whether a storage device and a key storage device are both coupled to a host. The account/password input unit receives an administrator ID and an administrator password. The ID acquiring unit obtains IDs of the storage device and the key storage device. The encryption unit encrypts the administrator ID, the administrator password, and the IDs of the storage device and the key storage device into encryption data. The protection control unit stores the encryption data into the key storage device and sets an access mode of the storage device as a protection status according to the administrator ID and the administrator password. Thereby, the storage device can be effectively unlocked by using the key storage device.