For the two typical topologies of the extra high voltage magnetically controlled shunt reactor (MCSR), this study introduces its specific wiring methods and working principles. It conducts an analysis of the change characteristics and response characteristics of the core magnetic flux under different wiring modes of the controlled shunt reactor body. Based on PSCAD, two typical structures are used to model the body of the first 500 kV MCSR put into operation in a provincial power grid and perform steady-state and dynamic simulations. The results of field experiments are compared and analyzed. The winding connection mode of the device’s body electromagnetic transient model is determined, which lays a foundation for the follow-up research.