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The hydrogen storage properties of the Scandium (Sc) atom modified Boron (B) doped porous graphene (PG) system were studied based on the density functional theory (DFT). For a single Sc atom, the most stable adsorption position on B-PG is the boron-carbon hexagon center after doping with the B atom. The corresponding adsorption energy of Sc atoms was −4.004 eV. Meanwhile, five H2 molecules could be adsorbed around a Sc atom with the average adsorption energy of −0.515 eV/H2. Analyzing the density of states (DOS) and the charge population of the system, the adsorption of H2 molecules in Sc-B/PG system is mainly attributed to an orbital interaction between H and Sc atoms. For the H2 adsorption, the Coulomb attraction between H2 molecules (negatively charged) and Sc atoms (positively charged) also played a critical role. The largest hydrogen storage capacity structure was two Sc atoms located at two sides of the boron-carbon hexagon center in the Sc-B/PG system. Notably, the theoretical hydrogen storage capacity was 9.13 wt.% with an average adsorption energy of −0.225 eV/H2. B doped PG prevents the Sc atom aggregating and improves the hydrogen storage effectively because it can increase the adsorption energy of the Sc atom and H2 molecule.