The increasing gross weight of electric Unmanned Aerial Vehicle (UAV) poses a chal-lenge in practical applications. The range and endurance of the electric UAV are limited by the fixed mass of the battery package. In this work, a design optimization method for the battery package topology of small electric UAV is proposed to enhance the performance. To improve the accuracy of the method, the dynamic battery model and simplified electric component models are presented. These models are utilized by the trajectory optimization method, which takes the dynamic charac-teristic into consideration to calculate the aircraft performance. The direct optimal control method is used for solving the trajectory optimization problem, and this method is tested on a small blended-wing-body electric aircraft. The test result shows that the range and energy-consumption are mainly influenced by the parallel topology of the battery package, while the flight time in climb phase is more sensitive to the series topology. It is deduced that the range- and energy-optimal design points can be considered concurrently in design optimization. The work proves the feasibility of integrating the trajectory optimization and battery package design.