In order to solve the problem in carrier UAVs of the coupling of attitude and trajectory in the longitudinal channel at the end of carrier landing, a decoupling control strategy was proposed by using the elevator channel to control the attitude and using the engine channel to control the trajectory. The control method made up of dynamic inversion and adaptive control was applied to weaken the influence of unknown disturbances and guarantee the rapidity of the control system. In order to reduce the landing error caused by deck motion, the deck motion compensation network was designed.The simulation results show that the control scheme has a satisfactory control effect, and the controller has strong anti-interference ability, which can effectively reduce the influence of the ship stern flow.