Structural vibrations of ultra-large structures during on-orbit assembly should be prevented to the maximum extent, given the extreme structural flexibility and low natural frequencies. The assembling process was divided into 4 stages: the grasping stage, the position-attitude adjusting and stabilizing stage, the mounting stage and the crawling stage. For the mounting stage, the dynamics and control were addressed, and a collinear assembly trajectory planning method was proposed to prevent structural vibrations. First, a dynamic model for the on-orbit assembly system including the main structure, the space robot and the assembling structure, was established based on natural coordinate formulation and absolute node coordinate formulation. Second, the requirements of collinear assembly were transformed into a trajectory planning problem of the space robot. The distance from the space robot mass center to the main structure should remain fixed, which is the main idea of the proposed collinear assembly method. Numerical simulation results show that, the proposed assembly method can effectively prevent the transverse motions of the ultra-large structure and reduce the required grasping moment. Finally, the influences of the system parameters on the dynamic responses during the assembly process were studied. The work provides a theoretical basis for the on-orbit assembly of ultra-large spacecraft.