A design method of a high energy efficiency unmanned aerial vehicle (UAV) green data acquisition system belongs to the technical field of data acquisition and optimization for UAV uplink communication. Firstly, a system optimization objective is constructed; and in a uplink communication network of a single UAV and ground sensors, the UAV receives data periodically. Secondly, according to a constructed optimization problem, the optimization objective is maximization of EE({W},{t},{S}). Finally, an original problem is decomposed into two approximate concave-convex fractional sub-problem based on a block coordinate descent method and a successive convex approximation technique to obtain a suboptimal solution; an overall iterative algorithm is proposed: in each iteration, by solving the sub-problems, wake-up scheduling S, time slot t and UAV trajectory W are alternately optimized. The solution obtained in each iteration is used as the input of next iteration. The present invention can jointly optimize the UAV flight trajectory, the sensor wake-up scheduling and the flight time slot to ensure that the transmission information amount and energy consumption of the sensors satisfy system requirements, while maximizing the energy efficiency of the system.