The invention introduces an apparatus for encrypting and decrypting user data, including a memory, a bypass-flag writing circuit and a flash interface controller. The bypass-flag writing circuit writes a bypass flag in a remaining bit of space of the memory that is originally allocated for storing an End-to-End Data Path Protection (E2E DPP), where the bypass flag indicates whether user data has been encrypted. The flash interface controller reads the user data, the E2E DPP and the bypass flag from the memory and programs the user data, the E2E DPP and the bypass flag into the flash device.