A high voltage protection system includes a high voltage processing circuit, a pulse width modulation signal outputting circuit, a driving circuit, and a coil module. The high voltage processing circuit is used for receiving and processing a high voltage. The pulse width modulation signal output circuit is coupled to the high voltage processing circuit for generating a pulse width modulation signal. The driving circuit is coupled to the pulse width modulation signal outputting circuit for receiving the pulse width modulation signal and generating a driving voltage accordingly. The coil module is coupled to the driving circuit and is operated according to the driving voltage.