A time clock signal processing system and method thereof, applicable to an environment of USB synchronous mode audio clock reconstruction, is disclosed. The clock signal processing method employed by the clock signal processing system first uses a first-stage phase-locked loops (PLL) to raise the frequency of the inputted USB start-of-frame (SOF) field, provides clock synchronization and outputs the second-stage PLL; then, the second-stage PLL reduces the timing jitter of the output of the first-stage PLL to below 20 ps.