The invention provides a serial compensation equipment protection system of a parallel structure. A spark gap and a bypass switch are connected between serial transformer windings, and when overvoltage occurs in serial compensation equipment and the spark gap reaches a fixed-value motion after a fault and before that the bypass switch is closed, the serial transformer windings are by passed, and overvoltage protection is carried out on the equipment. In the protection system, the spark gap cooperates with the bypass switch, coordinated overvoltage protection is carried out on the equipment, overvoltage stress is prevented from developing continuously, and the total reliability of the equipment is improved.