Using the difference Fourier analysis of neutron powder diffraction data along with first-principles calculations, we reveal detailed structural information such as methyl group orientation, hydrogen adsorption sites, and binding energies within the nanopore structure of ZIF8 (Zn(MeIM)(2)). Surprisingly, the two strongest adsorption sites that we identified are both directly associated with the organic linkers, instead of the ZnN4 clusters, in strong contrast to classical MOFs, where the metal-oxide clusters are the primary adsorption sites. These observations are important and hold the key to optimizing this new class of ZIF materials for practical hydrogen storage applications. Finally, at high concentration H-2-loadings, ZIF8 structure is capable of holding up to 28 H-2 molecules (i.e., 4.2 wt %) in the form of highly symmetric novel three-dimensional interlinked H-2-nanoclusters with relatively short H-2-H-2 distances compared to solid H-2. Hence, ZIF compounds with robust chemical stability can be also an ideal template host-material to generate molecular nanostructures with novel properties.