The electric sail (ES) is a novel propellantless propulsion concept, which extracts the solar wind momentum by repelling the positively charged ions. Due to the difficulty of attitude adjustment by the large flexible structure and the uncertainty of ion density, velocity and electron temperature by solar wind, there exist thrust input uncertainty and saturation with time-varying bounds for ES. The trajectory tracking problem for ES in three-dimensional (3-D) space is studied, and the composite sliding mode control scheme with corresponding guidance strategy is proposed for the single-input–multiple-output (SIMO) non-linear system. The hierarchical sliding surfaces are constructed with an auxiliary design system to analyse the effect of input saturation constraints and decouple the SIMO non-linear system to reduce the control complexity. Also, the disturbance estimation based on a super-twisting algorithm is employed to decrease the switch chattering and improve the system robustness. It is proved that all the sliding mode surfaces are asymptotically stable, and all the signals of the closed-loop system are bounded with input saturation constraints. Furthermore, all the signals are converging to zero and the closed-loop system is asymptotically stable without saturation. Finally, the simulation demonstrates the proposed composite sliding mode control is fit for ES 3-D trajectory tracking.