The present invention provides a design method of a high energy efficiency Unmanned Aerial Vehicle (UAV) communication system assisted by an intelligent reflecting surface, and belongs to the technical field of UAV communication network energy efficiency optimization. A communication process comprises two transmission links, one link is directly sent from an information source to an information sink, and the other link is reflected and transmitted by an intelligent reflecting surface attached to a UAV. The two links exist simultaneously. Based on an idea of block iteration, an original problem is decomposed into three sub-problems, and a non-convex optimization problem is transformed into solvable concave-convex fractional program problems by a continuous convex approximation technique. The present invention provides a design method for joint optimization of a passive beamforming of the intelligent reflecting surface, an active beamforming of a base station and a flight trajectory of the UAV.