In order to suppress surface dark current of electron multiplying CCDs, Shockley-Read-Hall theory is applied to describe the generation progress of surface dark current. The theoretical model of surface dark current is established by curve fitting. Recovery characteristic time of surface dark current is obtained through a quantitative analysis when the device is switched from inverted mode to non-inverted mode. Periodic inverted mode is proposed based on the timing character. Imaging clocks are modulated by periodic inverted pulses during signal integration. The device is switched from inverted mode to non-inverted mode at a period less than surface dark current recovery time. Simulation results show that surface dark current dramatically decreases as periodic inverted frequency increases. When the period equals 0.2 ms, average surface dark current is 0.051 nA/cm2, approaching inverted mode level. The results are in good agreement with theoretical analysis and the feasibility of periodic inverted mode is proved.