There exist complex disturbances in the attitude control system of flexible spacecrafts, such as space environmental disturbances, flexible vibrations, inertia uncertainties, payload motions, etc. To suppress the effects of these disturbances on the performance of attitude stabilization, a super-twisting disturbance observer (STDO)-based nonsingular terminal sliding mode controller (NTSMC) is proposed in this paper. First, STDO is designed for a second-order dynamical system constructed by applying the lumped disturbance and its integral as state variables, and applying the integral as virtual measurement. Since the virtual measurement is obtained by integrating the inverse attitude dynamics, STDO not only avoids the differential operation of angular velocity, but also fully utilizes the information of a nonlinear model. By combining STDO with NTSMC, a composite controller is designed to achieve high-accuracy spacecraft attitude stabilization. Since most of the disturbances are compensated for by a STDO-based feedforward compensator, only a small switching gain is required to deal with the residual disturbances and uncertainties. Thus, the chattering phenomenon of the controller can be alleviated to a great extent. Finally, numerical simulations for the comparison between STDO-based NTSMC and nonlinear disturbance observer-based NTSMC are carried out in the presence of complex disturbances to verify the effectiveness of the proposed approach.