A command processing method and a storage controller using the same are provided. The command processing method includes: receiving a plurality of I/O commands; categorizing the I/O commands into a plurality of groups according to a processor effort index of the I/O commands; selecting a first group from the groups, resetting a timer and obtaining an expiration time corresponding to the first group according to the I/O commands of the first group, and executing the I/O commands of the first group; and selecting a second group from the groups and resetting the timer when the expiration time of the first group expires, wherein when the processor effort index of the first group is less than a threshold, a clock frequency of the processor is lowered before the expiration time expires.