Considering carbon emission cost and consumer loyalty, this paper establishes a three-level multi-channel supply chain composed of the leading manufacturer, the retailer, and the consumer and builds a multi-channel supply chain with centralized decision-making and decentralized decision-making modes, and the optimal decision-making under both decision-making modes is solved. The study found that the carbon emission reduction level of multi-channel centralized decision-making is better than that of decentralized decision-making under the same carbon emission cost, and centralized decision-making can improve the carbon emission reduction level. Manufacturers open a direct channel to help reduce carbon emissions and need to consider the cost of emission reduction in their channel decisions. Consumer loyalty also directly impacts channel decisions. Only when carbon emission costs and consumer loyalty are within a reasonable range can new direct sales channels be opened to bring in new profits. Simultaneously, the total profit of the supply chain is greater than that of decentralized decision-making, but the double marginal utility of both parties decreases with the increase in carbon emission costs.