To promote carbon emission reduction and resource reuse, this study is devoted to studying the impact of government subsidy policies on the operation decision of a low-carbon closed-loop supply chain system. In the production stage, governments can use carbon reduction subsidies and remanufacturing subsidies to reduce the green behavior costs of manufacturers; in the recycling stage, governments can use consumer recycling subsidies to increase the recycling willingness of consumers. In this study, we introduce these three subsidy policies into the target function of the subsidized members. Using the Nash non-cooperative game and variational inequality, we developed a low-carbon supply chain network equilibrium model to examine the impact of subsidy policies on the system operation decision. The results show that, under the three subsidy policies, raising the subsidy level can help to improve the recycling rate, promote the reduction in carbon emissions and improve the profits of retailers; however, manufacturers’ incomes increase only when the carbon reduction subsidy level is below a certain threshold. Notably, under the coexistence of three subsidy policies, the carbon reduction subsidy policy has a more significant impact on the system. Finally, the numerical results show that, when the subsidy level is higher than six, although the increase in carbon reduction subsidy level leads to a decrease in the profits of manufacturers, this policy has the best contribution to the environmental benefits of the system. Our results can serve as guidelines for governments when designing the optimal subsidy programs to achieve the ultimate goal of establishing an environmentally friendly supply chain network system.