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