The conjugation of external species with two-dimensional (2D) materials has broad application prospects. In this study, we have explored the potential of noble metal/2D MOF heterostructures in hydrogen storage. Specifically, the MgH2-Ni-MOF@Pd system has shown remarkable hydrogen desorption/sorption performances, starting to liberate hydrogen at 181 °C, which is 230 °C lower than that of pristine MgH2. Under the catalytic effect of Ni-MOF@Pd, the dehydrogenation apparent activation energy of MgH2 is noticeably decreased from (133.5 ± 17.5) to (34.58 ± 1.87) kJ·mol−1, and the hydrogenation apparent activation energy is reduced from (70.41 ± 7.43) to (25.78 ± 4.64) kJ·mol−1, which is lowered by 63.4%. The fully-dehydrogenated MgH2-Ni-MOF@Pd composite rapidly uptakes hydrogen, with 2.62 wt% at 100 °C and 6.06 wt% at 150 °C within 300 s, respectively. The mechanism analysis of MgH2 catalyzed by Ni-MOF@Pd has revealed that the transformation of Mg2Ni and Mg2NiH4 could act as a “hydrogen pump”, providing numerous channels for fast diffusion and transport of hydrogen atoms. Moreover, in the dehydrogenation process, the element Pd reacts with MgH2 to form the Mg-Pd alloy phase, which makes MgH2 take precedence to decompose through the Mg-Pd alloy rather than self-decomposition, further reducing thermal stability and improving de/hydrogenation kinetics. The synergistic effect of Mg-Pd, Mg2Ni, and the special ultra-thin 2D sheet structure of the additive is the main reason for the good hydrogen storage property of MgH2-Ni-MOF@Pd. Our findings provide inspiration for designing efficient multi-functional additives with unique morphologies to optimize the hydrogen desorption/sorption behaviors of hydrogen storage materials.