A fan rotation speed control circuit of a power supply system is provided, which is applicable for controlling the rotation speed of the fan according to a loading state outputted by the power supply system. The fan rotation speed control circuit of the power supply system includes a waveform generating module, for generating an oscillating waveform signal; a current retrieving module, for retrieving a current signal corresponding to the loading state; a rotation speed control signal generating module, for comparing the oscillating waveform signal with the current signal, and generating a rotation speed control signal; a signal amplifying module, for amplifying an amplitude of the rotation speed control signal and outputting the amplified rotation speed control signal to the fan, so as to control the rotation speed of the fan.