In order to solve the problems of high coupling degree and poor scalability of the model, and support complex verification scenarios such as multi-energy collaborative optimization, dynamic condition testing and fault injection, in this study, a layered real-time simulation system based on NI PXIe dual real-time timing is designed. The model-policy decoupling architecture is innovatively adopted, and the system provides a virtual-real fusion verification platform with high dynamic response (millisecond level) for hybrid power systems. The lower layer runs a multi-physical field model, and the upper layer deploys energy management algorithms to achieve microsecond-level synchronous interaction through high-speed CAN communication. The system performance is outstanding: the interaction delay is less than 50 μs, the working condition switching error is less than 2%, and the verification efficiency is 40% higher than the traditional method. Its standardized tool chain and hierarchical architecture design have important reference value for the development of vehicle/ship hybrid power system, which can significantly improve the engineering credibility of strategy verification.