This paper investigates a fuzzy disturbance observer (FDO)-based terminal sliding mode control (TSMC) strategy for the liquid-filled spacecraft with flexible structure(LFS-FS) under control saturation. Firstly, a novel FDO is designed to estimate the lumped uncertainty, including the inertia uncertainty, external disturbance, the coupling of liquid slosh and flexible structure(LF), as well as the parts that exceed control saturation. The merits of the FDO lie in that estimation error can be arbitrarily small by adjusting the designed parameters and the prior information is not required. Then, based on the estimation of FDO, a finite-time TSMC is designed, which has more satisfactory control performance, such as chattering reduction and fast convergence speed. The stability of the closed-loop system is proved strictly by Lyapunov theory. Finally, numerical simulations are presented to demonstrate the effectiveness of the proposed method.