With increasing demands for hazard protection in nuclear safety of nuclear power plant, the complexity of protection systems design has increased sharply. Traditional document-based system engineering methods can no longer effectively meet the efficient, accurate, and reliable development requirements of hazard protection. Therefore, model-based system engineering (MBSE) methods have been introduced into the hazard protection development process. This paper proposed a turbine missile protection system modeling process based on requirements-function-logical-physical (RFLP) and MBSE, as well as a model system supporting the operation of this process. Based on this, the paper utilized a turbine missile protection development task as an example, and took the model as the core, providing the MBSE system modeling process and its model examples. The modeling of turbine missile protection requirements analysis, turbine missile protection function modeling, and turbine missile protection system architecture analysis and synthesis were elaborated. This demonstrated the advantages of the model-based design method in early verification of requirements, rapid simulation of functions, and data traceability in the development process of turbine missile protection system, thereby effectively enhancing R&D design efficiency.