The driving mechanism of the flapping wing aircraft is a critical component which affects the aircraft performance directly. However, in practical flights, the joint of the mechanism was found with non-uniform wear, in some cases leading to the failure of the mechanism. As an essential connection component, the joint has a crucial effect on the transmitting loads and the motion rules, but the clearance of the joint is unavoidable, it will affect the performance of the mechanism. At the same time, the contact collision force triggers non-uniform wear, accelerates the functional degradation of the mechanism, and impacts the safety of the mechanism. Therefore, a method for predicting non-uniform wear of joint considering multi-source random variables is proposed in this paper, and the flapping driving mechanism is taken as an example for joint wear prediction, and the validity of the method is verified by comparing with the practical experimental joint wear. In addition, the wear reliability and sensitivity of the flapping driving mechanism considering uncertainty are also investigated, and it provides guidance for the lifetime prediction and optimization design of the flapping driving mechanism.