The disclosure provides a clock step control circuit and a method thereof. The clock step control circuit includes a clock divider, a multiplexer, and a controller. The clock divider receives a first clock signal and outputs multiple second clock signals. The multiplexer receives the second clock signals and outputs one of the second clock signals. The controller is coupled to the clock divider and the multiplexer. When the controller receives an interrupt signal, the controller outputs a selection signal to the multiplexer according to the interrupt signal. The multiplexer outputs another one of the second clock signals according to the selection signal. The clock step control circuit and the method thereof in the disclosure can appropriately switch the clock signal to output a clock signal with an appropriate clock frequency.