During the on-orbit assembly of ultra-large space structures，transporting large flexible assembly modules to the docking position may induce significant structural vibrations.In this paper，a compliance control method based on input shaping is proposed to prevent the structural vibrations by analyzing the coupled dynamics of the space robot and flexible assembly module system.A coupled dynamics model of the space robot and assembly module system is established using the natural coordinate formulation and absolute nodal coordinate formulation （ANCF）.An input shaping feedforward control method is designed for the space robot handling the flexible assembly module.The numerical simulations show that the proposed modified input shaping （MIS） control method effectively suppresses the structural vibrations during the transportation，achieving fast and stable transportation.Compared with the commonly-used zero vibration and derivative （ZVD） shaper，the method proposed in this paper significantly reduces the transportation time and enhances the transportation efficiency.