As hydrogen molecules enter the clathrate hydrate body, the ubiquitous dodecahedral cavity (512) is too small to allow anything but single occupancy thermodynamically. The possibility that H2 double occupancy can occur in the dodecahedral cavity has been suggested and is still under debate. Here we uncover the unique feature of multiple occupancy of the hydrogen molecule in a dodecahedral cavity as induced by tuning the cage dimensions. The guest promoter population in the hydrate matrix spontaneously controls the degree of molecular hydrogen storage by tuning the cage dimensions. Our analysis combined with computational study reveals that only 1% expansion (3% in volume) of the cage dimensions is sufficient to provide thermodynamically stable room for double occupancy in the dodecahedral cavity. The findings in this research provide a strategy for doubling the hydrogen population in dodecahedral cavities in structure II hydrates.