The kinematic accuracy of space manipulator determines whether the spacecraft performs normally or not. Problems pertaining to structural deformation have received increased attention in recent times. In the space manipulator systems, flexible arms and joints can induce drastic dynamic instabilities. In applications such as the space station, kinematic error due to structural deformation can jointly affect the performance characteristics. And it is crucial for accuracy control of space manipulator to establish a precision index. Here we analyze the dynamics characteristic of flexible space manipulator considering the hysteresis of harmonic reducer based on method of nonconstraint boundary modal. For the sake of describing the output accuracy, we integrate the method of analytic hierarchy process(AHP) to establish a comprehensive evaluation index. A numerical simulation is performed to analyze the nonlinear dynamic characteristics of space manipulator with harmonic reducer. With the analysis of accuracy assessment, the relation among the hysteresis angle, rigidity and output accuracy is revealed. Considering the elastic modulus of flexible space manipulator and the hysteresis angle of harmonic reducer, we conduct an evaluation of output characteristics of flexible space manipulator with the proposed comprehensive evaluation index. The accuracy evaluation of output characteristics based on the proposed comprehensive evaluation index is implemented in the initial stage of space manipulator’s design, which can not only solve the problems existing in the design but also save cost savings for ground tests. The results can be used in designing and optimizing future space manipulators, which may provide valuable references for design and thermal control of the space manipulator. The kinematic accuracy of space manipulator determines whether the spacecraft performed normally or not. Problems in to the structural deformation have received attention in recent times. In the space manipulator systems, flexible arms and joints can induce drastic dynamic instabilities. In applications such as the space station, kinematic error due to structural deformation can can jointly affect the performance characteristics. And it is crucial for accuracy control of space manipulator to establish a precision index. Here we analyze the dynamics characteristic of flexible space manipulator considering the hysteresis of harmonic reducer based on method For the sake of describing the output accuracy, we integrate the method of analytic hierarchy process (AHP) to establish a comprehensive evaluation index. A numerical simulation is performed to analyze the nonlinear dynamic characteristics of space manipulator with harmonic reducer. With the ana lysis of accuracy assessment, the relation among the hysteresis angle, rigidity and output accuracy is revealed. consideration of the elastic modulus of flexible space manipulator and the hysteresis angle of harmonic reducer, we conduct an evaluation of output characteristics of flexible space manipulator with the recommended comprehensive evaluation index. The accuracy evaluation of output characteristics based on the proposed comprehensive evaluation index is implemented in the initial stage of space manipulator’s design, which can not only solve the problems existing in the design but also save cost savings for ground tests. The results can be used in designing and optimizing future space manipulators, which may provide valuable references for design and thermal control of the space manipulator.