Nonlinear pilot-induced oscillations (PIOs) pose a threat to the safety of piloted aircraft in flight. This study aimed to address this safety concern. A novel method for designing an assistance controller based on incremental model predictive control is proposed to aid pilots in suppressing categories 2 and 3 PIOs. In the assistance controller design, the characteristics of the full pilot–aircraft system are considered through a predictive model that integrates the dynamics of the pilot, actuator, and aircraft. This ensures that the assistance controller coordinates with both the pilot and aircraft. Additionally, an adaptive logic for the pilot–controller authority assignment is proposed to automatically adjust the role of the assistance controller. This adaptive logic adopts a model predictive technique to determine whether the pilot’s independent control will cause actuator saturation over the receding prediction horizon. By doing so, the assistance controller is restricted to work only when the actuator saturation constraints are activated. The pilot model-based simulations and the human-in-the-loop experiments demonstrated that the proposed assistance controller can effectively assist pilots in dealing with factors causing nonlinear PIOs while maintaining a harmonious cooperative relationship with the pilot.