The invention provides an intelligent protection circuit of a UPQC (Unified Power Quality Conditioner). A series current converter of the UPQC is connected between a load i1 and an electric power system US through a coupling transformer UC; a parallel current converter is connected between the load and the electric power system directly and located in a circuit which is arranged behind the coupling transformer; two ends of the coupling transformer are in parallel connection with an antiparallel silicon controlled rectifier SCR and a fifth circuit breaker CB5; two ends of the antiparallel silicon controlled rectifier SCR are provided with disconnecting switches; a first circuit breaker CB1 is connected with the connected position of the coupling transformer and the electric power system; a second circuit breaker CB2 is connected with the connected position of the coupling transformer and the load; a third circuit breaker CB3 is connected with the connected position of the series current converter of the intelligent protection circuit and the electric power system; a fourth circuit breaker CB4 is connected with the connected position of the parallel current converter of the intelligent protection circuit and the electric power system. The invention also provides an intelligent protection method of the UPQC. The intelligent protection circuit and method of the UPQC can achieve rapid and efficient fault protection on the UPQC.