The formation of magnesium hydrides through the chemical reaction between magnesium and hydrogen gas is considered one of the most effective hydrogen storage methods. During this reaction process, thermal management is crucial to maintain the reaction active because of the large amount of heat generated, but has been challenging due to the poor heat transfer in the powder bed. In this study, a novel reactor of tooth-shaped configuration is designed for Mg-based hydrogen gas storage, where the hydrogen is not only the stored gas but also serves as the cooling medium in direct contact with the Mg powders. The hydrogen gas in the reactor can flow uniformly through the interior of the Mg plate of compacted powders at a relatively high rate. The proposed direct contact cooling reactor with tooth-shaped configuration is studied numerically in comparison with another direct contact cooling reactor with parallel sheet configuration as well as the traditional reactor with a second cooling medium. The required reaction time for storage for the tooth-shaped configuration is 40% and 78% lower compared with that of the parallel sheet configuration and the traditional reactor, respectively. The reaction rate increases with higher flow rate of hydrogen gas, although at the cost of higher pumping power. When the hydrogen storage rate and the storage density of the total system are the main considerations, the tooth-shaped configuration with flow-through hydrogen demonstrates clear advantages over the other two reactors.