A clock generating device, method thereof and a computer system using the same are provided. The clock generating device includes a PLL module and a tuning module. The PLL module receives a reference clock signal, and generates an output clock signal as a basic clock of a computer system according to a phase difference between a reference clock signal and a feedback signal. The PLL module includes a frequency divider adjusting an intrinsic frequency dividing ratio according to a control signal and performs a frequency dividing processing on the output clock signal to generate a feedback signal. The tuning module coupled with the PLL module generates the control signal according to a VID of a CPU and one of the feedback signal and the reference clock. Therefore, the operation frequency of the components serving the output clock signal as the basic frequency in the computer system can be synchronously tuned.