A clock generation system having a time and frequency division activation mechanism is provided that includes a clock source processing circuit that generates a primary clock signal and clock-branching circuits that perform a clock-branching generation procedure respectively in an order. Each of the clock-branching modules includes a frequency division unit and a processing unit. The frequency division unit receives the primary clock signal to divide the frequency according to a divisor number and output a branch clock signal. The processing unit controls the frequency division unit to not output the branch clock signal before the clock-branching generation procedure and to decrease the divisor number gradually over time period after the clock-branching generation procedure begins such that a branch frequency of the branch clock signal generated by the frequency division unit increases from an initial frequency to a final frequency to finish the clock-branching generation procedure.