This study focused on the hierarchical modular approach to assembling space structures, which can be scaled up to increasingly larger sizes. This approach is based on dividing a large space structure into multiple modules, each with homogeneous automatic assembly functions. Hence, the overall structure can have diverse shapes and functions depending on the arrangement of modules, regardless of the size of the structure. Conventional approaches use locomotion and docking/release mechanisms installed on each module, but have been limited to 2-D shapes. In this study, a mechanism was developed that uses permanent magnets and electromagnets to assemble the space structure into any shape in three dimensions. The response surface method and downhill simplex method were used to optimize the size and arrangement of the magnets for efficient locomotion. The proposed mechanism was applied to a demonstration experiment to evaluate its effectiveness compared with existing methods.