Based on ab initio calculations, we have investigated the H-2 adsorption and storage capacity on boron-substituted and nitrogen-substituted nano-carbon materials doped with alkaline earth metal ions (Be2+, Mg2+, and Ca2+) systematically. The calculation results show that the Be2+-decorated, Mg2+-decorated, and Ca2+-decorated carbon-based materials with B-substitution and N-substitution improve the hydrogen storage capacity. H-2 molecules are bound stronger with lighter cations. The adsorption energy of H-2 molecule on the M2+-nano-carbon complex (M2+ = Be2+, Mg2+, and Ca2+) is disproportional to ionic radii of the M2+ cations. The interaction between H-2 and M2+@nano-carbon complex is elucidated by Mulliken charge analysis. It is determined that the highest gravimetric density is predicted to be 13.38 and 19.89 wt.% for the B-substituted and N-substituted materials, respectively. Copyright (C) 2015 John Wiley & Sons, Ltd.