A switch circuit for switching two clock signals includes a clock generator, a flip-flop and a multiplexer. The clock generator is to generate a reference signal whose cycle is the lowest common multiple of the cycles of the two clock signals. The flip-flop is to generate a selecting signal by taking a control signal from system as an input signal and taking the reference signal as a timing trigger signal. The multiplexer can output a selected clock signal according to the selecting signal in which the selected clock signal and the switched clock signal are synchronous during their entire cycles.