In the process of marine resource development and marine environmental protection, the government supervises the production behavior of enterprises; enterprises accept government supervision; and non-profit organizations supervise the process. On this basis, a conceptual model of the relationship between government, enterprises, and non-profit organizations is established, and the internal mechanism governing their interactions is analyzed. Using game theory, a simulation model of government, enterprises, and non-profit organizations is constructed, and a Nash equilibrium solution and strategy selection analysis are carried out. The correlation between the game participants and strategy selection is simulated and analyzed with MATLAB 7 software. Lastly, relevant countermeasures and suggestions are put forward to engender effective supervision by government departments, continuous environmental development and effective environmental protection of enterprises, and effective supervision by non-profit organizations. Studying the regulatory strategies of the government, enterprises, and non-profit organizations can provide a foundation for marine resource development and marine environmental protection policy in accordance with the current situation.