The optimization design of buildings is very important to the energy consumption, carbon emissions, and sustainable development of buildings. The low-temperature granary has a low grain storage temperature and high energy consumption indexes. The design scheme of the roof insulation for a low-temperature granary should be determined in actual building design processes by considering the costs, carbon emissions, and outdoor climate, comprehensively. In this paper, a new low-carbon optimization design method is proposed for the roof insulation in the low-temperature granary. The low-carbon optimization design method can respond to the cost issue, emission reduction issue, and outdoor climate issue, simultaneously. Moreover, the low-temperature granary roof insulation of different ecological grain storage zones in China is optimized in terms of carbon reduction by using the proposed low-carbon optimization design method. The application results of the optimization design method in different ecological grain storage zones in China indicate that the outdoor climate has significant impacts on the economic performance and carbon reduction effect of roof insulation. The cost considerations related to carbon emissions can apparently increase the economic efficiency of roof insulation. The optimal economic thicknesses of expanded polystyrene (EPS) in the cities of Urumqi, Harbin, Zhengzhou, Changsha, Guiyang, and Haikou are 0.025 m, 0.037 m, 0.085 m, 0.097 m, 0.072 m, and 0.148 m, respectively. The different outdoor climates of the seven ecological grain storage areas in China have important influences on the comprehensive economic performances of low-temperature granary roof insulation. The design of the low-temperature granary roof insulation in Haikou city has the best economic performance among the seven ecological grain storage zones in China.