The invention provides a protecting system of a unified power quality controller (UPQC) and a protection control method of the protecting system. An antiparallel silicon controlled rectifier is mounted on a primary side of a serial coupling transformer, and the rest five breakers are respectively mounted at the joint of the serial coupling transformer and the system, the joint of the serial coupling transformer and a load, the joint of a parallel part of the UPQC and the system, the joint of the serial part of the UPQC and the coupling transformer and on the primary side of the serial coupling transformer. The serial coupling transformer can be quickly bypassed within 10ms after short-circuit fault occurs on a load side and a system side, and protection on the UPQC coupling transformer and a serial side converter is realized; the serial coupling transformer can be quickly bypassed, system short-circuit impedance has no changes, and system upper-level fault protection action is unaffected; the controller can be secondarily protected through action of the breakers under the condition that the antiparallel silicon controlled rectifier fails to operate on command, and reliability and safety of the controller are improved.