Due to the limitation of the capacity of current rockets, the ultra-large space structures can’t be built by in-orbit deployment technique. In-orbit assembly is an effective way to construct these ultra-large space structures. In this paper, an ultra-large space structure is designed inspired by the Vicsek fractal, and the corresponding in-orbit assembly control strategy is proposed for intelligent spacecraft cluster. To describe the position and attitude motion of spacecraft during in-orbit assembly, the position and attitude dynamics equations of rigid spacecraft are built. Also, the relative motion parameters of the chaser spacecraft and target spacecraft are given. The assembly configuration of 125 spacecraft is designed based on Vicsek fractal structure which is divided into 3 stages, and each stage is further divided into two phases: pre-assembly and assembly. In the pre-assembly phase, the chaser spacecraft is expected to approach the target spacecraft with a small distance and maintain a relatively static state. After completing the pre-assembly, the controller drives the chaser spacecraft to slowly approach the target spacecraft, and the chaser spacecraft will dock with target spacecraft. For the pre-assembly phase, the compound controller with collision and PD controller is designed, and only PD control is used for the slow docking phase. Finally, the effectiveness of the control law for the assembly mission is verified by numerical simulation.