A multi-channel memory system has a memory device, a plurality of channels, and a control circuit. The memory device has a plurality of memory storage spaces. The channels are coupled to the memory storage spaces, respectively, wherein each of the channels is configured to act as a memory interface for accessing a corresponding memory storage space independently. The control circuit controls clock frequencies of clocks on the channels, respectively. At a same time point, the channels include at least a first channel operating at a first clock frequency set by the control circuit and a second channel operating at a second clock frequency set by the control circuit at a same time point, and the second clock frequency is different from the first clock frequency.