We have investigated functionalized 2D carbon allotrope, graphdiyne (GDY), as a promising hydrogen storage media. Density functional theory with a range of vdW corrections was employed to study Ni decoration of pristine and boron-doped GDY and the interaction of resulting structures with molecular hydrogen. We showed that boron-doped GDY is thermally stable at 300 K, though, its synthesis requires an endothermic reaction. Also, boron doping enhances Ni binding with the graphdiyne by increasing the charge transfer from Ni to GDY. Ni doping drastically influenced hydrogen adsorption energies: they rise from ~70 meV per H2 molecule on pristine GDY to a maximum of 1.29 eV per H2 becoming too high in value for room temperature reversible applications. Boron doping improves the situations: in this case, after Ni decoration desorption temperature estimation is ~300–500 K. Overall, each Ni adatom on B-doped GDY can bind only one H2 molecule within the needed energy range, which gives low hydrogen uptake (~1.2 wt%). However, doping with boron led to the decrease in the value of hydrogen adsorption energy and good desorption temperature estimations, therefore, codoping of metal atoms and boron could be an effective strategy for other transition metals. © 2020 The Authors