This paper proposes a control system for bi-copter subject to model uncertainties. A comprehensive model of bi-copter is established with analysis of mass change, center of gravity shift and actuator dynamics. For handling the center of gravity shift, a nonlinear disturbance observer considering the actuator dynamics is designed in rotational loop to estimate the lumped disturbance. The disturbance estimation is fed into the attitude controller. In the translational loop, an incremental nonlinear dynamic inversion (INDI) based controller is utilized to track desired trajectory while dealing with the negative effects of mass uncertainty. Comparative studies on simulations and flight tests validate the effectiveness of the proposed methods and the robustness of the system has shown a significant improvement in the presence of mass change and center of gravity shift.