This paper uses the differential game approach to construct a model of cooperative emission reduction involving the government, manufacturing firms, and retail firms under different power structures. It is found that the dominant player receives more subsidies; the development of a mechanism for horizontal technology R&D among enterprises can reduce the financial pressure on the government to implement compensation strategies and improve the effectiveness and performance of supply chain emission reduction; and the government can develop differentiated subsidy schemes to achieve Pareto optimality in the supply chain and environmental performance based on different game strategies and revenue-sharing agreements by enterprises.