The unified right confirmation and registration of natural resources in sea areas (URCRNRSA) has been considered a key approach to the effective management and sustainable utilization of marine resources. In China, the system of URCRNRSA is insufficient due to the lack of central auditing supervision and public participation. In this study, the mechanism of stakeholder interaction is clarified based on the game relationship among the tripartite of the central government, local governments, and the public. The evolutionary process of tripartite decision-making is simulated with an evolutionary game model. On this basis, the strategic choices of the tripartite were analyzed in the four evolutionary scenarios of high-quality URCRNRSA. It was demonstrated that the tripartite could jointly affect the URCRNRSA through cooperation-constraint, principal-agent, and incentive-compatibility relationships. The most effective, realistic, and feasible URCRNRSA strategy was the trinity system with local government high-quality rights confirming, the central government auditing as a hard constraint and the public participating as a soft constraint. The main influencing factors for the tripartite to make different strategy selections were clarified through parameter sensitivity analysis, including cost, benefit, reward, and punishment. Accordingly, the policy recommendations were put forward to ensure the stable and efficient implementation of the URCRNRSA in China.