The invention provides a method of managing SDIO commands at a host device and a peripheral device. The host device connected to the peripheral device by a bus comprising a command transmission line and a data transmission line, both of which are arranged to transmit single end signal. The host device converts operation requests into converted commands and combines a first SDIO complied data packet with the converted commands to generate a first combined data packet. Then, the host device transmits the first combined data packet through the data transmission line, wherein the first combined data packet comprises a first header for indicating whether the first combined data packet comprises the converted commands. After receiving the first combined data packet, the peripheral device parses the first combined data packet to obtain the converted commands, and then performs processing procedures according to the converted commands.