Abstract: Ultra-large spacecraft can reach the kilometer scale and are composed of hundreds of structural modules, mainly constructed through on-orbit assembly and on-orbit deployment. Existing research in this field has mainly concentrated on a limited number of assembly and deployment processes for conventional-sized space structures, whereas investigations about the orbital and attitude dynamic behaviors involved in the assembly and deployment of kilometer-scale ultra-large space structures remain scarce. This paper proposes a modeling method for the attitude and orbital coupling dynamics of variable-configuration rigid bodies based on the natural coordinate formulation for the on-orbit assembly and deployment process of kilometer-scale ultra-large space structures. Firstly, the geometric description of the variable-configuration rigid body in natural coordinates is given, the mass matrix and kinetic energy expression are derived, and the dynamic modeling method of the variable-configuration rigid body is proposed based on constrained Hamilton’s equations. The effectiveness of the modeling method is verified through two variable-length pendulum examples, including a uniformly varying length example and a uniformly accelerated varying length example. Then, the attitude and orbital coupling dynamics model of the variable-configuration rigid body during on-orbit deployment and assembly is established, and the attitude and orbital coupling dynamic responses of the variable-configuration process of the space truss during on-orbit deployment are studied. The theoretical expression of the Coriolis moment is derived, which is consistent with the variation law of the attitude control moment during the deployment process in numerical simulation. Finally, based on the proposed modeling method, the orbit-attitude coupled dynamics of the deploy-after-assembly construction strategy of ultra-large space structures is studied. The assembly sequence using two space robots is designed based on four principles such that the space structure is symmetry and the gravity gradient torque is almost zero during the assembly process. In this case, the Coriolis moment becomes the main disturbance moment.