The complexity of the functional modules in the platform architecture of virtual reality simulation system puts forward higher requirements for software system platform design. The performance requirements, such as expansibility and portability, real-time and interoperability, and human-computer interaction are the problems to be solved urgently. Taken the case of underwater engineering as the design basis, the optimization of an agent-oriented virtual reality simulation platform is proposed based on high-level architecture (HLA). According to the underwater operation process, a whole life cycle concept design is conducted. The system function and design principles are analyzed and clarified. Based on HLA technical framework, the virtual reality technology is used as the function-oriented module to partition the simulation system, and the federal architecture is given. Through the case of practice simulation, the optimization performance is verified. The results show that the virtual reality simulation platform plays a good performance of expansion, real-time, interoperability, human-computer interaction and other functional characteristics. In addition, the application of middle layer and multi-layer technology improves the flexibility and conciseness of the system architecture greatly.