Metal–organic frameworks (MOFs) are a novel family of physisorptive materials that have exhibited great promise for methane storage. So far, a detailed understanding of their methane adsorption mechanism is still scarce. Herein, we report a comprehensive mechanistic study of methane storage in three milestone MOF compounds (HKUST-1, PCN-11, and PCN-14) the CH4 storage capacities of which are among the highest reported so far among all porous materials. The three MOFs consist of the same dicopper paddlewheel secondary building units, but contain different organic linkers, leading to cagelike pores with various sizes and geometries. From neutron powder diffraction experiments and accurate data analysis, assisted by grand canonical Monte Carlo (GCMC) simulations and DFT calculations, we unambiguously revealed the exact locations of the stored methane molecules in these MOF materials. We found that methane uptake takes place primarily at two types of strong adsorption site: 1) the open Cu coordination sites, which exhibit enhanced Coulomb attraction toward methane, and 2) the van der Waals potential pocket sites, in which the total dispersive interactions are enhanced due to the molecule being in contact with multiple “surfaces”. Interestingly, the enhanced van der Waals sites are present exclusively in small cages and at the windows to these cages, whereas large cages with relatively flat pore surfaces bind very little methane. Our results suggest that further, rational development of new MOF compounds for methane storage applications should focus on enriching open metal sites, increasing the volume percentage of accessible small cages and channels, and minimizing the fraction of large pores.