In this paper, an intelligent autonomous deck landing system is designed for an Unmanned Air Vehicle (UAV). First, the design specifications and requirements are identified for the design of UAV flight control and landing systems. Then the longitudinal models of the UAV are established for the design of an autonomous UAV landing system. The system is designed using fuzzy logic, which is able to provide longitudinal stability and to improve the tracking performance. Simulation results show that the developed landing control system has very good robustness against aerodynamic uncertainty, and good fault tolerance against actuator failures. This indicates that the intelligent landing system has the ability to stabilize a damaged aircraft without knowledge of the types of fault or system parameters. Wind disturbances are also investigated by using the turbulence model for the ship-landing environment. The simulation results show that the designed landing system is robust against the wind disturbances. Landing of a UAV on the deck of a ship is conducted. Various automatic landing scenarios are simulated. These scenarios consider the ship motion induced by environmental disturbances, the impact of the wind disturbances on the UAV, and aero variations. Simulation results show that the designed intelligent automatic ship landing control system can land the UAV on the deck of an ocean-going ship automatically, accurately and safely. The system is very robust against massive disturbances and uncertainties (ship heave motion, wind disturbances, and aero variations).