A negative voltage protection system includes a negative voltage comparison circuit, a signal processing circuit, a driving circuit, a driving output circuit, a power device, and a coil module. When the coil module generates a back electromotive force, the coil module outputs a negative voltage. When an intensity of the negative voltage detected by the negative voltage comparison circuit is greater than a predetermined value, the signal processing circuit generates a control signal to the driving circuit. The driving circuit controls the driving output circuit and the power device to reduce the intensity of the negative voltage according to the control signal.