This paper considered the physical-layer security of information transmission in an unmanned aerial vehicle(UAV) multi-user communication system, where a UAV communicated with multiple users on the ground, with the presence of an eavesdropper on the ground trying to intercept the confidential information sent from the UAV to the users. It modeled the channels between the UAV and all ground nodes as more accurate probabilistic LoS(line-of-sight) channels. This paper studied maximizing the minimum average secrecy rate of all users by jointly designing the 3D trajectory of the UAV and the user scheduling, under the constraints of UAV fight conditions and the discrete user scheduling parameters. To solve the optimization design problem for the UAV secure communication system under the probabilistic LoS channel model, this paper first decoupled it into three sub-problem, then solved the three sub-problems one by one, by using the integer relaxation and successive convex approximation methods, and finally obtained the 3D flight trajectory of UAV by using the block coordinate descent method. Based on the instantaneous channel state information obtained during the UAV's flight, it further proposed a real-time optimization algorithm for UAV speed and user scheduling. This algorithm formulated the optimization problem into a linear programming problem and solved it by using the interior point method. Simulation results show that compared to the existing benchmark algorithms, the trajectory optimization of UAV based on the probabilistic LoS channel model can significantly improve the secrecy rate of the system, and the proposed real-time optimization algorithm for speed and user scheduling can further improve the secrecy rate performance.