In smart substations, it is difficult to identify the faulty component quickly and effectively in the secondary circuit of protection systems. In view of this, a fault diagnosis method for secondary circuits of protection systems in smart substations is proposed to find faulty components accurately. First, the physical-loop and virtual-loop models of the secondary circuit are established according to the SCD file, and their mapping relationship is implemented. Secondly, a fault proof table is used to obtain the suspicious fault component set in secondary circuits of protection systems. Then, improved D-S evidence theory is proposed to evaluate the components in the suspicious component set, and the probability of secondary circuit failure caused by each component is obtained for the realization of fault component identification. Finally, case studies demonstrate that the proposed method can deal with excessive conflict of component self-checking evidence, find fault component accurately, and supply reference for the operation and maintenance of protection systems. This work is supported by National Natural Science Foundation of China (No. 51877084), Natural Science Foundation of Hebei Province (No. E2018502063), and Fundamental Research Funds for the Central Universities (No. 2017MS096).