The cheap price of carbon sink trading in certification emission reduction (CER) makes it more popular than the carbon emission allowance (CEA); trading in carbon-neutral, enterprises are more inclined to purchase carbon sinks to achieve their own carbon neutrality goals and promote decarbonization of the whole chain. Companies urgently need to figure out how to achieve carbon neutrality with government rewards and punishments. Moreover, as an important factor affecting the effectiveness of supply chain, it is particularly important to study how to coordinate fairness concerns of such objects. Therefore, a centralized and two-stage Stackelberg game model of a closed-loop supply chain (CLSC) of one manufacturer and one retailer is constructed, and the cost-sharing contract, revenue-sharing contract, and cost–revenue-sharing contract are used to coordinate it, taking into account the fairness concerns of downstream enterprises while pursuing carbon neutrality, ensuring the overall benefits of the supply chain, and considering the impact of government subsidies and rewards and punishments on the carbon neutrality of the supply chain. Research shows that (1) compared with the other two contracts, the cost–revenue-sharing contract performs better and can effectively achieve the Pareto optimum; (2) the cost-sharing contract performs better in accomplishing the carbon neutrality of the CLSC; (3) excessively high carbon sink prices are not only detrimental to enterprise efficiency, but also to the realization of carbon neutrality goal; and (4) higher supply chain utility is pursued by enterprises when the unit reward and punishment are not great enough; otherwise, carbon neutrality is pursued. The research results can not only provide decision support for the product pricing, carbon sink reserve and contract design of CLSC enterprises under the goal of carbon neutrality, but can also provide a reference for the setting of government subsidies and rewards and punishment.