The invention provides a method for achieving tooth space compensation for a flexible joint of a space manipulator. The method comprises the following steps that the position command signals yd of a direct current motor and the position signals y output by a kinetic model, with space influences taken into consideration, of the flexible joint of the space manipulator are collected, a sliding mode variable structure controller is designed, and a sliding-mode control law is obtained; the control input of a control system of the flexible joint after linear decoupling processing is carried out is obtained by adopting a differential geometry feedback linearization method according to the sliding-mode control law; according to the control input of the control system of the flexible joint after linear decoupling processing is carried out, a disturbance observer is designed for the kinetic model, with the space influences taken into consideration, of the flexible joint of the space manipulator, the control input, under compensation space nonlinear influences, of the flexible joint, and therefore it is guaranteed that the position output of the control system tracks the expected position signals with needed precision. According to the technical scheme of the method for achieving the tooth space compensation for the flexible joint of the space manipulator, influences of the space on the system position precision can be compensated for effectively, high-precision tracking control can be achieved, and the happening frequency of the buffeting phenomenon is reduced at the same time.