The invention discloses a virtual and real loops association mapping and diagnosis method of a virtual and real diagnosis system of an intelligent substation, and the method comprises an association mapping method of a process layer virtual and real loops and a diagnosis method of the process layer virtual and real loops; the association mapping method of the process layer virtual and real loops comprises the following steps: 1, building a real loop model; 2, building an association relation between the real loop and a message block, namely defining a sending port and a receiving port, and a sent or received message block APPID; 3, building the association relation between the port and a virtual loop broken link warning signal, port power and port state warning signal; 4, storing the configured association relation in a secondary operation and maintenance model file; 5, parsing a SCD model and the secondary operation and maintenance model, and storing the model association relation ina library. The association relation of the real loop and the virtual link is built, and technical problems, such as failure in building of process layer virtual and real loops mapping and implementation of diagnosis of process layer virtual and real loops, of the virtual and real loops of the intelligent substation are solved.