The magnesium-based hydrogen storage alloy has a very good prospect to be applied in the market of lightweight automobile due to its merits of light weight, excellent discharge performance, long cycle life, and large hydrogen storage capacity. However, existing studies on magnesium-based hydrogen storage alloy have a series of shortcomings such as the insufficient works in terms of model reasonability analysis, heat transfer behavior analysis, heat control scheme design, and comparative experiment analysis, etc. In view of these problems, this paper studied the thermal effect and heat control strategy of the Mg-based Hydrogen Storage Alloy (MHSA) system for lightweight automobile. At first, this paper constructed numerical models for the fluid-solid coupled heat exchange region and the heat conduction region in the system; then, based on the law of energy conservation, a heat transfer behavior model of the MHSA system was established and used to analyze the thermal effect of the system. After that, according to the driving process of hydrogen fuel cell electric vehicle, the working process of the MHSA system was further analyzed to study the heat control process. Next, this paper proposed a new idea for the heat control of the MHSA system, gave a few tips for the simulations, and presented the flow of the heat control scheme of the system. At last, the experimental results were given and analyzed.