Hydrogen can play a central role in a fossil-free energy economy, yet its implementation is hindered by the lack of safe, dense, and efficient storage methods. Hybrid H₂ physisorption-hydrate formation, which combines physisorption in porous materials with encapsulation in clathrate hydrates, presents a promising route, but the fundamental synergistic mechanisms remain largely elusive. Here, we perform microsecond-scale molecular dynamics simulations to study the hybrid H₂ storage process in the hydrophobic metal–organic framework ZIF-8 seeded with THF hydrate nanoparticles. The results indicate that ZIF-8 rapidly physisorbs H₂, while effectively excluding H₂O and THF. Our simulations reveal a dynamic, three-step hybrid storage pathway, i.e. , (1) ZIF-8 selectively adsorbs and enriches H₂ within its pores, creating a high local H₂ concentration; (2) The growing binary H₂-THF hydrate crystals selectively capture the H₂; (3) Transfer of H₂ from the ZIF-8 to the hydrate until the hydrogen source transfer reaches a dynamic equilibrium. This hybrid storage method results in a total H₂ storage capacity reaching 1.82 wt%, exceeding the storage capacity of either physisorption or THF-driven hydrate formation alone. These findings provide critical molecular-level insights, showing that coupling hydrophobic ZIF-8 with hydrate promoters is a highly effective strategy for developing next-generation H₂ storage methods.