This paper presents a new guidance and control system based on an adaptive backstepping method for a space transportation system. In recent years, many studies of flight control systems using feedback linearization combined with time-scale separation have been carried out. Since this type of control system does not depend on the design points along a predetermined trajectory, the designed system can be applied to an extensive flight region. However, in this method, control performance tends to deteriorate with changes in the control gains and parameters because it is difficult to guarantee the stability of the system. Additionally, since it is not easy to obtain prior knowledge about disturbances and aerodynamic characteristics, an estimation mechanism must be added to the system. To solve this problem, we propose an adaptive flight control system combining feedback linearization, the backstepping method, and disturbance observers. A disturbance observer is effective for estimating the effect of extraneous signals. In the proposed system, by appropriately redesigning the disturbance observer, it becomes possible to guarantee the stability of the entire system, including the estimation mechanism. Numerical simulations were performed to verify the effectiveness and robustness of the proposed system when applied to an automatic landing problem.