This paper constructs a decision-making model of a dual-channel supply chain based on different carbon trading policies and discusses the impact of different carbon quota allocation methods adopted by the government on the dual-channel supply chain. Under the restriction of carbon quota trading policy, with the goal of maximizing enterprise profit, the paper compares and analyzes the influence of carbon emission quota and carbon trading price on the profits of dual-channel supply chain and obtains the optimal decision-making model of enterprise channel selection. The example calculation shows that the profit level of manufacturers and retailers will be significantly affected by different carbon quota allocation policies along with the development of channels. The profit of manufacturers is positively correlated with the amount of carbon allowances, and the relationship with carbon trading price shows different trends under different allocation policies of carbon allowances. The retailer’s profit in the dual channel is not affected by the amount of carbon quota and the price of carbon trading, and the relationship between the retailer’s profit and the amount of carbon quota and the price of carbon trading in the single channel shows different trends under different carbon quota allocation policies.