Based on ab initio calculations, we have investigated the H2 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. H2 molecules are bound stronger with lighter cations. The adsorption energy of H2 molecule on the M2+‐nano‐carbon complex (M2+ = Be2+, Mg2+, and Ca2+) is disproportional to ionic radii of the M2+ cations. The interaction between H2 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 © 2015 John Wiley & Sons, Ltd.