Under the government subsidy policy, this paper introduces shareholding cooperation strategy into the supply chain emission reduction decision, and applies differential game theory to study the optimal decision and dynamic coordination of the supply chain. A centralised decision model and a decentralised decision model before and after the shareholding partnership are constructed, and the effects of the shareholding ratio and consumers' low-carbon preferences on the optimal decision, profit and government subsidy policy are analysed. The results of the study show that the shareholding strategy replaces part of the government subsidy policy, and the closer the supply chain members cooperate, the more effective the government subsidy is. As the shareholding ratio increases, the total profit of the supply chain changes in a “U” shape, and only when the shareholding ratio meets certain conditions are supply chain members willing to choose shareholding cooperation, and the implementation of shareholding cooperation strategy can achieve supply chain coordination. The government, as the policy maker, is not influenced by consumers' preference for low carbon emissions.