Aiming at the problem of trajectory planning and task allocation for eVTOL multi-aircraft cooperative emergency delivery in low-altitude economic scenarios, a two-layer planning model nested in each other is proposed. The upper layer model makes task allocation decisions at the macro level, and is modeled with the objective function of minimizing the total delivery time, and two solution algorithms are designed based on the ant colony algorithm according to two commonly used task allocation ideas. In the lower level, the objective is to minimize the total cost of multi-UAVs to perform the mission, establish the spatio-temporal coordination mechanism, and introduce the quantum genetic algorithm to solve the eVTOL multi-UAV trajectory planning by combining with the task allocation decision of the upper level model. Finally, simulation analysis is carried out, and the results show that the paths planned by this paper’s method are shortened by at least 6.4% compared with the GWO model. Compared with the traditional genetic algorithm, the average value of the total cost of synergy of the quantum genetic algorithm used is optimized by 1.66%. In the planning environment of this paper, the algorithm solution efficiency and quality are optimal when the cost weights of each sub-objective are 0.45 and 0.65, respectively, and the population size is 200.