It is a promising way to construct large-scale space structures, such as large antennas or space telescopes after the modular units of space structures are launched in a stacked manner and then assembled in orbit by space robots. However, there exist the following problems that have to be considered or solved for a successful task in the process of space robot on-orbit assembly of space structure module units, including dynamic models regarding the free-flying space robots and the complex contact scenario, difficult control of docking force/torques considering different docking scenarios, and substantial uncertain interference during the docking process. Given the above difficulties, this paper analyzes the on-orbit assembly contact scenario of multi-module units, builds the dynamic model of space robot for on-orbit assembly tasks and addresses the three-dimensional space contact dynamic model. Further, the authors adopt an adaptive impedance control method based on a reference model to control the docking forces. This method adjusts the compliance trajectory in real-time according to the force tracking error value to adapt to complex working conditions and resist external interference so that the contact force can accurately track the expected value, thereby ensuring the successful docking of module units and avoiding damage to the mechanical structure caused by physical contact. A simulation platform is constructed to numerically verify the modeling and control methods regarding to the whole in-orbit assembly process. Then ground experiment platforms are established to validate the dynamic model of the free-flying space robot and force control method of the space robot during its assembly process. The experimental results show that the adaptive impedance control method still presents good force control performance and environmental adaptability in complex contact scenarios where single-module units or multi-module units are synchronously docked. This method can be applied to force control in the on-orbit assembly process of space large-scale structures such as (super) large-aperture space optical combination mirror group.