The development of efficient hydrogen storage materials is crucial for advancing hydrogen-based energy systems. In this study, we prepared a highly innovative palladium-phosphide-modified P-doped graphene hydrogen storage material with a three-dimensional configuration (3D Pd3P0.95/P-rGO) using a hydrothermal method followed by calcination. This 3D network hindering the stacking of graphene sheets provided channels for hydrogen diffusion to improve the hydrogen adsorption kinetics. Importantly, the construction of the three-dimensional palladium-phosphide-modified P-doped graphene hydrogen storage material improved the hydrogen absorption kinetics and mass transfer process. Furthermore, while acknowledging the limitations of primitive graphene as a medium in hydrogen storage, this study addressed the need for improved graphene-based materials and highlighted the significance of our research in exploring three-dimensional configurations. The hydrogen absorption rate of the material increased obviously in the first 2 h compared with two-dimensional sheets of Pd3P/P-rGO. Meanwhile, the corresponding 3D Pd3P0.95/P-rGO-500 sample, which was calcinated at 500 °C, achieved the optimal hydrogen storage capacity of 3.79 wt% at 298 K/4 MPa. According to molecular dynamics, the structure was thermodynamically stable, and the calculated adsorption energy of a single H2molecule was −0.59 eV/H2, which was in the ideal range of hydrogen ad/desorption. These findings pave the way for the development of efficient hydrogen storage systems and advance the progress of hydrogen-based energy technologies.