Mg-based materials have been investigated as hydrogen storage materials, especially for possible onboard storage in fuel cell vehicles for decades. Recently, with the development of large-scale fuel cell technologies, the development of Mg-based materials as stationary storage to supply hydrogen to fuel-cell components and provide electricity and heat is becoming increasingly promising. In this work, numerical analysis of heat balance management for stationary solid oxide fuel cell (SOFC) systems combined with MgH2 materials based on a carbon-neutral design concept was performed. Waste heat from the SOFC is supplied to hydrogen desorption as endothermic heat for the MgH2 materials. The net efficiency of this model achieves 82% lower heating value (LHV), and the efficiency of electrical power output becomes 68.6% in minimizing heat output per total energy output when all available heat of waste gas and system is supplied to warm up the storage. For the development of Mg-based hydrogen storage materials, various nano-processing techniques have been widely applied to synthesize Mg-based materials with small particle and crystallite sizes, resulting in good hydrogen storage kinetics, but poor thermal conductivity. Here, three kinds of Mg-based materials were investigated and compared: 325 mesh Mg powers, 300 nm Mg nanoparticles synthesized by hydrogen plasma metal reaction, and Mg50Co50 metastable alloy with body-centered cubic structure. Based on the overall performances of hydrogen capacity, absorption kinetics and thermal conductivity of the materials, the Mg nanoparticle sample by plasma synthesis is the most promising material for this potential application. The findings in this paper may shed light on a new energy conversion and utilization technology on MgH2-SOFC combined concept.