With dealing with the independent processing of multi-level long circuit in the process of black start, the distribution characteristics of the sequence voltage and the sequence current of the system under different operation modes are analyzed in detail. It proposes a fault identification method in this paper. The method selects likely fault buses by comparing buses sequence voltage. Then the fault identification method on comparison of amplitude and incidence matrix of sequence current calculated by sequence voltage and current and line parameter is proposed to judge the position. This algorithm needn’t to setting again. It could be immune to various complex conditions and it can not be mistakenly operated when the over-voltage generated by the charging of the no-load line. This fault identification algorithm can be used as backup protection in the normal system and it also can be setted as main protection in the single supply mode of black-start system.