This paper proposes a fixed-time anti-saturation (FT-AS) control scheme with a simple control loop for the 6-Degree-of-Freedom tracking (6-DOF) control problem of spacecraft with parameter uncertainties, external disturbances and input saturation. Considering the external disturbance and parameter uncertainties, the dynamical model of the tracking error is established. The traditional methods of handling input saturation usually add anti-saturation subsystems in the control system to suppress the impact of input overshoot. However, this paper directly inputs the input overshoot into the tracking error model, thus constructing a modified lumped disturbance term that includes the influence of input overshoot. Then, a novel fixed-time disturbance observer (FT-DO) is designed to estimate and compensate for this modified lumped disturbance. Therefore, there is no need to add the anti-saturation structures in the control loop, significantly reducing the complexity of the system. Finally, an observer-based fixed-time non-singular terminal sliding mode (FT-NTSM) controller is designed to guarantee the fixed-time stability of the whole system. In this way, the convergence time of the proposed scheme does not depend on the system’s initial conditions. Simulation results illustrate that the proposed method keeps the control input within the limit while achieving high-precision tracking control of attitude and position.