An effective combination of host and guest molecules in a framework type of architecture can enhance the structural stability and physical properties of clathrate compounds. We report here that an organic clathrate compound consisting of a fullerene (C60) guest and a hydroquinone (HQ) host framework shows enhanced hydrogen-storage capacity and good structural stability under pressures and temperatures up to 10 GPa and 438 K, respectively. This combined structure is formed in the extended β-type HQ clathrate and admits 16 hydrogen molecules per cage, leading to a volumetric hydrogen uptake of 49.5 g L–1 at 77 K and 8 MPa, a value enhanced by 130% compared to that associated with the β-type HQ clathrate. A close examination according to density functional theory calculations and grand canonical Monte Carlo simulations confirms the synergistic combination effect of the guest–host molecules tailored for enhanced hydrogen storage. Moreover, the model simulations demonstrate that the lithium-doped HQ clathrates with C60 guests reveal exceptionally high hydrogen-storage capacities. These results provide a new playground for additional fundamental studies of the structure–property relationships and migration characteristics of small molecules in nanostructured materials.