A system and a method for driving a motor with a frequency conversion mechanism are provided. The system includes a look-up table module, an oscillator circuit, a multi-frequency signal generator circuit, and a motor driver circuit. The look-up table module stores a preset driving signal. The oscillator circuit generates oscillating signals having different frequencies. The multi-frequency signal generator circuit outputs a multi-frequency signal according to the oscillating signals. One waveform segment of the multi-frequency signal in a modulation region has a first oscillating frequency. Another waveform segment of the multi-frequency signal outside the modulation region has a second oscillating frequency lower than the first oscillating frequency. When a back electromotive force or a phase current of the motor reaches zero within a time interval of the modulation region, the motor driver circuit drives the motor according to the preset driving signal and the multi-frequency signal.