In this study, we examined the robust super-twisting sliding mode backstepping control (SBSC) method, which employed a tracking differentiator and nonlinear disturbance observer for a hexacopter unmanned aerial vehicle (UAV) system. To realize robust tracking control performance for a highly coupled nonlinear hexacopter UAV system, a super-twisting sliding mode control method was combined with designing stabilizing controls of backstepping control (BSC) applied to the UAV system. Furthermore, the differentiation issue of the virtual control and compensation of transformation error in the conventional BSC design were bypassed via a new continuous tracking differentiator structure. Additionally, a new disturbance observer based on the proposed tracking differentiator was considered to estimate uncertainties of the hexacopter UAV. Comparative simulation results demonstrated that the proposed tracking-differentiator-based SBSC scheme (PTSBSC) blended with the tracking differentiator and nonlinear disturbance observer exhibits improved performance when compared to that of conventional BSC and disturbance observer systems.