The present disclosure relates to a power supply system for improving plasma uniformity and a method thereof, wherein the power supply system includes a signal generating device, a first electrode and a second electrode. The signal generator is respectively connected with a plurality of signal processing circuits and is used for generating a plurality of initial signals at different frequencies; the signal processing circuits are used for processing the initial signals at corresponding frequencies; the plurality of signal processing circuits are all connected with the first electrode; and the initial signals are processed by the signal processing circuits and then act on the plasma through the first electrode. The present disclosure may effectively process signals in different power supplies, improve the stability of plasma discharge, reduce the impact of the coupling effect between different power supplies, and realize the independent control of ion flux and ion energy.