In view of the entrusted transportation management model (ETMM) of China’s high–speed railway (HSR), the supervision strategy of an HSR company for its multiple agents plays a very important role in ensuring the safety and sustainable development of HSR. Due to the existence of multiple agents in ETMM, the supervision strategy for these agents is usually difficult to formulate. In this study, a quadruplicate HSR safety supervision system evolutionary game model composed of an HSR company and three agents was established through the analysis of the complex game relationship existing in the system. The behavioral characteristics and the steady state of decision–making of all stakeholders involved in the system are proved by evolutionary game theory and system dynamics simulation. The results show that there will be long–term fluctuations in the strategies selected by the four stakeholders in the static reward–penalty control scenario (RPCS), which indicates that an evolutionary stable strategy does not exist. With increases in the reward–penalty coefficient, the fluctuations are intensified. Therefore, the dynamic RPCS was proposed to control the fluctuations, and the simulation was repeated. The results show that the fluctuations can be effectively restrained by adopting the dynamic RPCS, but if the coefficients are the same, the static RPCS is better than the dynamic RPCS for increasing the safety investment rate of the three agents. This demonstrates that the HSR company should apply these two control scenarios flexibly according to the actual situation when formulating a supervision strategy in order to effectively control and enhance the safety level of HSR operations when multiple agents are involved.