China has been building an ecological compensation system to eliminate the contradiction between economic development and ecological protection. Aiming at conflicts of interest in the implementation of an ecological compensation policy for China’s mineral resource development, this study established a tripartite evolutionary game model to simulate the ecological compensation scenario and determined the evolutionary stable strategy (ESS) under different scenarios; it uses numerical simulation to analyse the strategy evolution process of stakeholders and the influence of parameter changes on each strategy. The results show that there is an optimal ESS for ecological compensation for mineral resource development, which condition is C1 < Ti + F1, P < F2, C2 < R1 + R2. The initial cooperation intentions of stakeholders directly affected the final stable state. Local governments are most affected by the input cost, and mining enterprises are most affected by the supervision of the central government. Punishment can effectively restrain the behavior of local governments and mining enterprises and promote the implementation of ecological compensation systems. In addition, the higher supervision cost of the central government, the longer time it will take for the stakeholders to reach the stable state. Finally, reducing the payment amount for ecological compensation will not affect the trend in environmental improvement; in contrast, it is conducive to the preservation of enterprises’ strength, economic development and ecological environment protection. The main findings of this study can help secure coordinate between the stakeholders in conflict and jointly formulate appropriate ecological compensation policy.