Neutral sections in AC electrified railway lead to transient problems such as overvoltage, overcurrent, pantograph-catenary arc and so on. In recent years, a flexible automatic neutral section passing technology had been proposed, and it was expected to solve the problems caused by neutral sections. On the basis of introducing the structure and working process of flexible automatic neutral section passing system, the small step and large step models of real-time digital simulator (RTDS)were used to model and simulate the flexible automatic neutral section passing system, and the process of train passing through the phase separation was simulated. In the simulation, power control was used to reduce the breaking current between pantograph and contact line, and frequency conversion phase shift was used to realize the flexible transition of neutral phase. The simulation results showed that the flexible automatic neutral section passing system could realize the train through electric phase continuously without power and voltage shocks.