This work focuses on the three-dimensional integrated guidance and control (IGC) problem for a flight vehicle with a body-aligned strapdown seeker. The strapdown seeker cannot provide the line-of-sight (LOS) angular rate information and causes difficulties in the controller design. Additionally, external disturbance and gain–loss actuator faults also lead to the loss of control performance. To solve these problems, an extended state observer (ESO) is firstly developed to estimate the LOS angular rate by applying the observed body-line-of-sight angles provided by the body-aligned strapdown seeker. Based on backstepping and dynamic surface control techniques, the fault-tolerant IGC is then designed to deal with the gain–loss actuator fault, and adaptive approaches are applied to improve the robustness of the system. Finally, the uniformly ultimately bounded stability of the flight control system is guaranteed via Lyapunov synthesis, and numerical simulations are conducted to verify the effectiveness of the system.