Kaolinite can be used for many applications, including the underground storage of gases. Density functional theory was employed to investigate the adsorption of hydrogen molecules on the kaolinite (001) surface. The coverage dependence of the adsorption sites and energetics was studied systematically for a wide range of coverage, Θ (from 1/16 to 1 monolayer). The three-fold hollow site is the most stable, followed by the bridge, top-z and top sites. The adsorption energy of H2 decreased with increasing coverage, thus indicating the lower stability of surface adsorption due to the repulsion of neighbouring H2 molecules. The coverage has obvious effects on hydrogen adsorption. Other properties of the H2/kaolinite (001) system, including the lattice relaxation and changes of electronic density of states, were also studied and are discussed in detail.