A computer system and overclock controlling method and program thereof, which includes steps of providing an overclock work voltage to a CPU when overclock is requested, then the CPU adjusts its clock domain according to the overclock work voltage. The overclock work voltage is a sum of a normal work voltage and an additional external voltage, by which the CPU may enter an overclock mode (a frequency of a clock domain signal is higher than a standard frequency value). Eventually, when the frequency of the clock domain signal of the CPU is in a stable status during the overclock mode, the work voltage for the CPU is reduced and the CPU keeps working in the overclock mode.