To solve the problems of time consuming and manual work in fault location of the traditional relay protection system, the paper presents research on an intelligent positioning method for relay protection. First, the main types of faults in the relay protection system of a smart substation are analyzed, providing theoretical support for fault simulation experiments. Secondly, the faults are simulated using PCS-978, and the data from experiments are collected to build a database, providing data support for the intelligent positioning method. Then, based on the experiments, the fault location matrix and table are designed. Finally, an intelligent positioning method based on a deep neural network is proposed, incorporating SMOTE and a random forest algorithm. The empirical results demonstrate that the intelligent location method can improve the efficiency of fault diagnosis in a smart substation protection system, can help relay protection technicians locate faults quickly and accurately, and is practical. This work is supported by the National Natural Science Foundation of China (No. 51607036).