With the gradual formation of "Trunk-Branch" linkage multi-level air cargo transportation system, the problem of low turnover efficiency of airport cargo is becoming more and more prominent, and the " Trunk-Branch" linkage efficient cargo allocation methods have become one of the key technologies to solve the above problems. In this study, an integer programming linkage allocation model was established with the maximum loading rate under "Trunk-Branch" linkage as the optimization objective while simultaneously satisfying constraints such as cabin position, cabin size, center of gravity, and weight for both trunk and branch aircraft. This model was applied based on genetic algorithms to optimize the cargo allocation between the B757-200 trunk aircraft and the ARJ21-700F branch aircraft. It was found that the average loading rate of "Trunk-Branch" linkage allocation was increased by 5.45% to 72.05% compared with sequential allocation.By demonstrating that the proposed "Trunk-Branch" linkage allocation method in this study can significantly increase the overall cargo loading capacity, and thus effectively improving the efficiency of cargo turnover at airports, laying a theoretical foundation and providing technical support for the safe and efficient development of the "Trunk-Branch" linkage multi-level air cargo transportation system.