Nuclear reactor engineering is a typical multidisciplinary and interdisciplinary complex system engineering with complex technology and high reliability requirements. Model based system engineering (MBSE) is recognized as one of the most likely design techniques to meet the needs of complex systems engineering in the digital context. This paper focuses on the internal requirements of R&D and design of nuclear reactor and coolant system, and discusses the application and role of model-based system engineering design method in the R&D of PWR. By discussing the design method of MBSE, the advantages of MBSE are compared and explored. The MBSE modeling of the PWR nuclear reactor and coolant system is carried out. The functional behavior analysis of the system is carried out by using the positive design concept, and the system functional decomposition and overall architecture design are completed, which can guide the tradeoff design and scheme optimization of the functional architecture of nuclear reactor and coolant system.