Incremental nonlinear dynamic inversion (INDI) methodology offers robustness against disruptions and benefits systems with model uncertainty. While the INDI does not provide the necessary control inputs, it does provide the amount of change of control input variation. As a result, the control input can swiftly adapt and yet precisely follow the trajectory even in the presence of unknown external disturbances. Built on the SE(3) using the geometry control technique, the proposed control rule is able to prevent the unwinding behaviors found in the quaternion-based attitude representation and the singularity inherent in the attitude representation based on Euler angles. Finally, numerical simulation results are shown to validate the effectiveness of the proposed control system. The closed loop system’s stability is proven by a Lyapunov-based analysis.