A method of managing operation commands for a flash memory includes: providing a first command queue for receiving and storing a plurality of normal operation commands; providing at least one word line read (IWLR) command queue for receiving and storing a plurality of IWLR operation commands; issuing a lock state command between each two consecutive IWLR operation commands to the at least one second command queue; determining a selected command queue from the first command queue and the at least one IWLR command queues according to the lock state command; and delivering an operation command from the selected command queue to the flash memory.