Hydrogen energy is viewed as a promising green energy source because of its high energy density, abundant availability, and clean combustion results. Hydrogen storage is the critical link in a hydrogen economy. Using first-principles density functional theory calculations, this work explored the role of B and N in modulating the binding properties of transition metal-modified graphene. The hydrogen storage performance of Sc-, Ti-, and V-modified B-doped graphene was evaluated. Boron doping induces an electron-deficient state, enhancing interactions between transition metals and graphene. Sc, Ti, and V preferentially adsorbed at the carbon ring’s hollow site in B-doped graphene, with their binding energies being 1.87, 1.74, and 1.69 eV higher than those in pure graphene, respectively. These systems can stably adsorb up to 5, 4, and 4 H₂ molecules, with average adsorption energies of −0.528, −0.645, and −0.620 eV/H₂, respectively. The hydrogen adsorption mechanism was dominated by orbital interactions and polarization effects. Among the systems studied, Sc-modified B-doped graphene exhibited superior hydrogen storage characteristics, making it a promising candidate for reversible applications.