Ultra-low homogeneous magnetic fields are essential for many areas of scientific research. To enable the realization of ultra-low homogeneous magnetic field, magnetically shielded room (MSR) is employed to shield the geomagnetic and environmental magnetic noises. A group of homogeneous magnetic field coil (HMFC) enclosed by the MSR is then used to generate ultra-low homogeneous magnetic field in a certain zone. Since the presence of MSR will significantly influence the field distribution of the HMFC, proper cooperation between MSR and HMFC is crucial for reducing the volume of the entire facility. In this paper, the theoretical magnetic field analysis model of HMFC based on MSR was constructed by the image method. By adopting a new optimization design method, the space-efficient configurations of HMFC based on MSR were proposed, and the validity of the analytical model was numerically verified. The optimized system parameters were normalized to scale the given results for any desired ultra-low homogeneous magnetic field. We show that to generate the same ultra-low homogeneous magnetic field, the system volume of the proposed structure is only 1%–83.3% of that of the traditional Merritt coil configurations. In general, this work paves the way for the space-efficient apparatus design for ultra-low homogeneous magnetic field generation.