The invention discloses a distribution automation factory master station joint debugging simulation system in the field of power grids. The system comprises physical transformer stations to be connected, a three-phase relay protection tester and a master station. All incoming and outgoing lines of the physical transformer stations to be connected are connected with the three-phase relay protection tester. The three-phase relay protection tester is connected to a switch. The switch is connected to a router. The router is connected to a host. The host simulates the simulated connection between the physical transformer stations to be connected and respective simulating transformer stations and the simulated connection between the respective simulating transformer stations. Each simulating transformer station corresponds to one conventional physical transformer station. The distribution automation factory master station joint debugging simulation system solves a problem that system power outage is required in conventional distribution automation system master-factory-side debugging access, improves power supply reliability, and solves a technical difficulty in verification of distribution network automation system FA strategy using a simulating power grid fault method.