The invention describes a switching power supply system for automatically regulating an operating frequency and the method. The switching power supply system has a sensing and monitoring unit connected to the computer system for detecting the operating status of the computer system and outputting a detection value, a setting unit for setting a trigger condition value, a storage unit connected to the setting unit for storing the trigger condition value, a comparator unit connected to the storage unit and the sensing and monitoring unit for comparing the detection value with the trigger condition value and outputting a comparison result signal, and a PWM switching frequency regulator unit connected to the comparator unit and the converter for receiving the comparison result signal and regulating the operating frequency of the pulse width modulation so that a converter can supply power to the computer system more efficiently.