Metal-organic frameworks (MOFs) are thought to be a set of promising hydrogen storage materials; however, little is known about the interactions between hydrogen molecules and pore walls as well as the diffusivities of hydrogen in MOFs. In this work, we performed a systematic molecular simulation study on the adsorption and diffusion of hydrogen in MOFs to provide insight into molecular-level details of the underlying mechanisms. This work shows that metal-oxygen clusters are preferential adsorption sites for hydrogen in MOFs, and the effect of the organic linkers becomes evident with increasing pressure. The hydrogen storage capacity of MOFs is similar to carbon nanotubes, which is higher than zeolites. Diffusion of hydrogen in MOFs is an activated process that is similar to diffusion in zeolites. The information derived in this work is useful to guide the future rational design and synthesis of tailored MOF materials with improved hydrogen adsorption capability.