Nonlinear model-based Hybrid Controller (NHC) is developed which consists of the adaptive proportional-integral-feedforward (PIF) gains and variable structure controller. The controller has the robustness against modeling uncertainty and is applied to the trajectory tracking control of single-input, single-output nonlinear systems. The essence of the scheme is to divide the control into four different terms. Namely, the adaptive P-I-F gains and variable structure controller are used to accomplish the specific control actions by each terms. The robustness of the controller is guaranteed by the feedback of estimated uncertainty and the performance specification given by the adaptation of PIF gains using the second method of Lyapunov. The variable structure controller is incorporated to regulate the initial peak of the tracking error during the parameter adaptation is not settled yet. The newly developed NHC method is applied to the power tracking control of a nuclear reactor and the simulation results show great improvement in tracking performance compared with the conventional model-based control methods.