At present, there are problems in the process of fault location and cause analysis in the actual work of substations, such as long time consumption, high investment in manpower and material resources, and low returns. A Digital Twin (DT) system construction method that can be used for virtual mapping in substations is proposed to address this problem. Firstly, the design principles and overall structure of the substation DT system were formulated by comprehensively considering the needs of transient modeling, debugging, and verification calculations in the substation. Then, the construction method and process of the three-dimensional twin model of the primary system (PS) in the substation were analyzed by using SolidWorks and Unity3D, and the graphical modeling method and process of the general protection and secondary circuit logic modules were analyzed by using the Cybersim integrated simulation support system. Finally, a three-dimensional twin model of the PS and secondary system (SS) equipment inside the substation was constructed. The reliability of the proposed method was verified through simulation experiments, and the results showed that the fault identification accuracy, fault location accuracy, and fault cause judgment accuracy were the highest during bus faults, with 96.10%, 94.17%, and 92.93%, respectively. The capacitor had the lowest accuracy, with 94.86%, 92.96%, and 91.73%, respectively. The DT system can accurately achieve functions such as status viewing and alarm of the substation, precise positioning and navigation of equipment, and positioning of faulty and abnormal equipment.