The design of thermal insulation in roofs is very important to reduce energy consumption and decrease the environmental impacts of buildings. An integrated economic and environmental assessment-based optimization design method is presented in this paper to find the best candidate insulation design scheme for building roofs, including the determination of roof thermal insulation type and the optimum insulation thickness. In the optimization design method, a zonal method-based double-skin ventilation roof heat transfer model is developed to predict the roof energy consumption. Economic and environmental benefits due to thermal insulation are calculated by using the economic analysis model, the environmental analysis model, and roof energy consumption. Moreover, an integrated dimensionless economic and environmental assessment index is proposed to evaluate different roof thermal insulation design schemes. The optimum insulation thickness is determined by maximizing the sum of economic benefit and environmental benefit due to thermal insulation. The validation results in a real building show that the predicted data for the zonal-based double-skin ventilation roof heat transfer model agreed well with the measured data, with a maximum relative error of 8.2%. The optimum insulation thickness of extruded polystyrene (EPS), mineral wool (MW), and polyurethane (PU) was between 0.082 m and 0.171 m for the single-skin roof in a low-temperature granary in Changsha region in China. The ranking of the integrated assessment indexes of thermal insulation is EPS > MW > PU. A double-skin ventilation roof can reduce the optimum thickness of thermal insulation. The best result is obtained by EPS for the double-skin roof with a grey outer surface color for the low-temperature granary roof in Changsha region in China. The influencing factors of insulation type, roof structure, and roof outer-surface color should be considered in finding the best candidate insulation design solution for building roofs. The integrated economic and environmental assessment-based optimization design method can help designers to efficiently find the best design scheme of thermal insulation to maximize the sum of economic benefit and environmental benefit for building roofs.