In order to realize the intensification of urban logistics operation, at the same time, the interruption of logistics supply and demand caused by emergencies shall be reduced as much as possible.Take logistics node positioning and channel layout as the foothold, the multi-objective programming of three-level hub and spoke logistics network is studied. Considering the structural constraints of hub and spoke network and the connectivity constraints between multi-level nodes, taking the location of multi-level hub and spoke points, the connectivity and strength between hub and spoke points as decision variables, and taking the minimum network construction cost and the maximum network tenacity as objective functions, a three-level hub and spoke logistics network model is constructed. Combined with the characteristics of the model, a genetic algorithm with double-layer structure is designed, in which the outer layer is a niche Pareto genetic algorithm with three-stage coding structure for solving multi-objective programming, and the inner layer is a genetic algorithm with 0-1 coding for solving network tenacity. Taking 14 node cities in a region as an example, the effectiveness of the model and algorithm is verified, and the optimization results are compared with two kinds of traditional single objective logistics networks. The results show that bilevel genetic algorithm can effectively solve the three-level hub and spoke logistics network planning model. Select the Pareto optimal solution obtained by case calculation to participate in the comparative analysis. Compared with the traditional three-stage hub and spoke logistics network, the optimization results have improved the network toughness by 6 times, but will bring a certain increase in network construction costs. Compared with the logistics network whose optimization goal is to maximize the flexibility, the network construction cost is reduced by 7 times, and the network flexibility is also reduced. It can be seen that the proposed dual objective three-stage hub and spoke logistics network model achieves the balance between network construction cost and network toughness, which has reference and application value for planners pursuing hub and spoke logistics network with certain invulnerability.