In response to the problem of traditional freight route network designs focusing solely on economic objectives while neglecting environmental impacts, a comprehensive optimization method for freight route network considering both economic goals and environmental effects was proposed in the context of green aviation. Based on a multi-allocation strict hub-and-spoke route network, a mathematical model was constructed with the objectives of minimizing economic costs, CO2, CO and Nox emissions. Linear weighting method and branch-and-bound algorithm were employed for solution in conjunction. The results indicate that there are certain differences in the route network structures under different optimization objectives, making it challenging to simultaneously achieve optimality. Compared to solutions that only consider economic costs, the comprehensive solution proposed in this paper achieves a better balance between economic benefits and environmental impacts.