Switching model is one of the key factors that affect the accuracy and efficiency of electromagnetic transient (EMT) simulation of power electronic systems. For the numerical oscillation problem of classical LC binary equivalent switch model, an improved method has been developed by adding a pair of virtual resistors with the same resistance and opposite symbols to the equivalent circuit and applying the exponential difference method. The new method has the advantages of invariable system admittance matrix, easy selection of equivalent parameters, and good numerical stability. Based on the proposed method, a Simulink toobox is developed to automatically generate the circuits’ calculation matrix according to the Simulink block diagram. An application example of a power electronic transformer is completed. Compared with the Simulink/SimPowerSystem model, the steady-state error of the proposed method is less than ±2%, and the simulation speed can be increased by tens of times, which shows practical value in the EMT simulation of multi-switch power electronic systems.