The invention relates to an H-bridge based permanent magnet switch drive control method and system. According to the method, an opening or closing request receives no response in default delay time after opening or closing stops, specifically, time interval between forward drive and reverse drive of the H bridge is increased, delay time difference of hardware is compensated, and when the forward drive or the reverse drive stops and a processor performs the next drive, the former drive stops completely. With the adoption of the method, corresponding software can be formed and stored in a storage and is operated by the processor of an H-bridge drive device, the processor and the storage are combined to form the permanent magnet switch drive control system, and the system is used for solvingthe problem of damage to an H-bridge hardware circuit due to unilateral conduction of the H bridge because of forward or reverse drive overlapping during switching of opening and closing states of thepermanent magnet switch controller.