In the context of the environmental improvement of inland shipping, this paper studies the interaction mechanism of tripartite behavioral strategy selection among the upstream and downstream governments and shipping companies in neighboring provinces. This paper constructs a tripartite evolutionary game model that introduces the prospect theory, and verifies numerical examples in combination with system dynamics simulation methods. Therefore, this study discusses the influence of evolutionary stability strategies on the development of electric ship industry. The results show that in order to realize effective governance of inland shipping pollution, the optimal evolutionary stability strategies of the three stakeholders should be as follows: active supervision in both upstream and downstream governments, and using clean energy in shipping companies. The improvement of the initial probability and risk preference of the three parties is conducive to promoting the faster and more stable industrial development, while reasonable profit distribution coefficient and compensation cost can promote the benign development of the inland river environmental governance system. In addition, the probability of upstream and downstream governments and shipping companies choosing the optimal strategies is positively related to the government fines, and negatively related to the regulatory costs. In particular, the application of prospect theory makes the result of evolutionary equilibrium more obvious.