This paper examines a farmer’s channel selection in a supply chain led by a retailer, considering carbon emissions and products’ deterioration. Three channels—online channels, retail channels, and dual channels—are proposed. The inventory model of perishable products and the two-stage Stackelberg game model are used to illustrate the operational process. To compare performances of the three channel structures, we further determine the critical points consisting of the profits and the carbon emissions among these channels. The results provide useful insights for supply chain members and the government. Farmers can choose a channel to optimize profit with respect to deterioration rate and product yield, but it might conflict with the aim of least carbon emissions. When the deterioration rate is high, the online channel is not a suitable choice. For the government, the carbon tax contributes to the reduction of carbon emissions, but it also leads to the loss of the farmer’s profit. Additionally, numerical results further illustrate that, from the perspective of the government, transporting and inventory processes are two major sources of emissions, and it is essential to implement carbon tax and exploit low-carbon transportation.