In this paper, the robust adaptive control of tilt-rotor aircraft is addressed using a hierarchical control augmentation system designed with specific focus on enabling robust operation under highly aerodynamically challenging environments such as shipboard environments. The control designs are based on backstepping and θ-D based control techniques. The adaptive control augmentation system is designed to provide high robustness to time-varying system parameters and disturbance effects from the environment to provide good disturbance attenuation properties in highly aerodynamically challenging environments. The control system is structured with a modular and hierarchical architecture combining adaptive trajectory tracking, model following, and motion planning modules and provides flexibility and customizability for various tilt-rotor aircraft configurations and operating environments. The overall control system and its constituent algorithms are designed to support both stand-alone operation and operation in conjunction with a human pilot or an existing baseline controller in a control augmentation fashion to provide additional robustness and reliability improvements under severe aerodynamic disturbance conditions. The robustness, stability, and performance of the proposed control algorithms are demonstrated through simulation based studies.