The invention relates to a method for controlling an index time-varying slide mode of flexible spacecraft characteristic shaft attitude maneuver, and belongs to the technical field of spacecraft control. The method comprises the steps that firstly, a system dynamically equivalent model, a dynamic model and a flexible vibration model are established under a spacecraft system, then, the vibration frequency and the damping ratio parameter of a closed loop system with the index time-varying slide mode control law are calculated, and a single-shaft multi-modality filtering input shaping device with a characteristic shaft as a rotary shaft is designed according to the designing method of the single-shaft input shaping device to restrain flexible vibration in three-shaft motion. Meanwhile, a state observer is designed to estimate flexible modal information in real time, and the method for controlling an output feedback index time-varying slide mode is formed. At last, saturability analysis is conducted on control torque so as to satisfy the physical saturation constraint of the control torque. By means of the method, the application range of existing input shaping is expanded, the input shaping technology is expanded from single-shaft maneuver to three-shaft maneuver, the self-robustness of filter input shaping is enhanced, and the purpose that the attitude maneuver path of the spacecraft is the shortest is achieved.