Aiming to design the three-dimensional trajectory tracking controller for hypersonic gliding vehicle under external disturbances, this paper presents a decoupling control strategy. The longitudinal height controller is designed based on proportional-derivative and the lateral line-of-sight (LOS) tracking controller is proposed based on terminal sliding mode. Firstly, the dynamic model of hypersonic gliding vehicles is presented. Then, the three-dimensional trajectory tracking problem is divided into longitudinal and lateral plane. Each waypoint is tracked using the height controller and the LOS tracking controller based on adaptive circle of acceptance, respectively. Finally, considering external disturbances, the LOS tracking based on sliding mode control (SMC) with power reaching law is designed and the stability of the closed-loop control system is proved. The Common Aero Vehicle (CAV) is used in numerical simulation, and the simulation results shows that under the influence of external disturbance, the trajectory tracking controller designed in this paper can track three-dimensional waypoints with high precision and stability.