Abstract: The development of deep-sea mineral resources has brought significant ecological and environmental challenges while alleviating the shortage of key metals. Therefore, how to effectively internalize environmental costs has become a core issue that urgently needs to be addressed. This paper focuses on the different stakeholders involved in deep-sea mineral resource exploitation, constructing a two-layer game analysis framework to analyze the internalization mechanism of environmental costs in deep-sea mineral resource exploitation. The first layer reveals through the Stackelberg game model between International Seabed Authority （ISA） and resource development enterprises that the environmental tax mechanism increases the cost of environmental damage for enterprises, guides them to independently increase environmental investment, reduce resource exploitation intensity, and achieve the coordination of economic and ecological benefits. The second layer game model further constructs a tripartite game model among resource development enterprises, environmental protection organizations, and ISA. Analysis shows that the combination of performance bond system and progressive pollution tax policy significantly increases the potential cost of corporate violations and effectively enhances corporate compliance incentives. At the same time, the supervision mechanism of environmental organizations increases the probability of discovering violations, further strengthening the tendency of enterprises to actively comply with environmental standards. On this basis, this paper proposes policy recommendations to improve the internalization of environmental costs for deep-sea resources, including establishing a combination policy system of “franchise fees + environmental taxes”, improving the performance bond and environmental protection fund system, strengthening international regulatory cooperation and information transparency mechanisms, in order to provide theoretical references and policy paths for sustainable governance of international deep-sea resource development.