AbstractThis study used periodic density functional theory and grand canonical Monte Carlo simulations to investigate the effects of the co‐doping of B and N atoms and substituting Zn2+ with Mg2+ or Ca2+ in the organic linker groups of MOF‐650. The functionalization increased the polarity of the organic groups, stabilizing the interaction between the MOF and hydrogen molecules. The highest average binding energy of the adsorbed hydrogen in MOF‐650 NB‐C7‐azulene‐Mg was calculated to be −4.75 to 5.40 kcal/mol for the α adsorption sites. Using the substitution of NB azulene and metal cations being Mg2+ or Ca2+, The hydrogen storage capacity of functionalized MOF‐650 was increased to 22 mg/g at 90 bar/298 K, implying the modification strategy of MOF‐650 would strengthen the interaction between MOF frameworks and hydrogen molecules.