A control apparatus with multiple flash memory card channels includes a host side port unit, an instruction data processing unit, and flash memory card port units. The host side port unit exchanges a host side instruction and host side read/write data with a high-speed serial communication protocol host side. The flash memory card port units respectively exchange flash memory card instructions and flash memory card read/write data with a plurality of flash memory cards. An instruction from the high-speed serial communication protocol host side is divided into multiple sub-instructions to be respectively transmitted to the flash memory card port units and exchange of instruction and data with a plurality of flash memory cards is carried out in a coincident period of time so as to achieve the purposes of expanding access capacity and increasing access speed, reducing the operation cost of products, and enhancing flexibility of use of flash memory cards.