Considering that microgrid (MG) can be controlled flexibly, its short circuit-current is limited and power flow is bidirectional. The paper presents a new relay protection scheme of microgrid based specific harmonic injection method. The injective harmonic flows all over microgrid and the amplitude of specific harmonic current will enhance in fault occasion. So the above characteristic can solve the problem of fault position and the symmetric characteristic can complete the identification of fault type. The discussion about the compatibility of microgrid protection and conventional distribution network line protection. At last, the combined microgrid model is built in Matlab/Simulink environment. The simulation result demonstrated that the above method can complete the identification of fault position and type and it also can coordinate with the traditional line protection well.