In this letter, we investigate an unmanned aerial vehicle (UAV) communication system, where an intelligent reflecting surface (IRS) is deployed to assist in the transmission from a ground node (GN) to the UAV in the presence of a jammer. We aim to maximize the average rate of the UAV commnunication by jointly optimizing the GN’s transmit power, the IRS’s passive beamforming and the UAV’s trajectory. However, the formulated problem is difficult to solve due to the non-convex objective function and the coupled optimization variables. Thus, to tackle it, we propose an alternating optimization (AO) based algorithm by exploiting the successive convex approximation (SCA) and semidefinite relaxation (SDR) techniques. Simulation results show that the proposed algorithm can significantly improve the average rate compared with the benchmark algorithms. Moreover, it also shows that when the jamming power is large and the number of IRS elements is relatively small, deploying the IRS near the jammer outperforms deploying it near the GN, and vice versa.