The strategy of combining non-noble metal core and carbon shell can produce a synergistic effect through interface engineering and simultaneously promote the activity and stability of materials. Heteroatomic doping can effectively regulate the band structure of graphene. Besides, the doping of phosphorus increases the distance between the metal alloy cores and is accompanied by the contraction of the D bandgap, the Fermi level near the density-of-states (DOS) is enhanced, which makes it have the characteristics of precious metals. Therefore, the design of heteroatomic-doped graphene-coated phosphorus-doped metal core–shell structure will effectively improve the electrocatalytic performance. Here, we use Prussian blue as the precursor to prepare the transition metal binary alloy and ternary alloy coated with multi-layer nitrogen-rich graphene shell by direct annealing in an inert atmosphere. Further, the core–shell nanostructure was converted to phosphorus-doped FeCoMo ternary alloy core through phosphating, in which phosphorus plays the role of bridging the ternary alloy and N-doped graphene shell, which is beneficial to improve the HER performance. The optimal material FeCoMo@NG-P exhibited excellent catalytic performance for HER in both 1.0 M KOH and 0.5 M H₂SO₄, reaching a current density of 10 mA cm⁻² at low overpotentials of 170 mV for the alkaline solution and 196 mV for the acid solution, and the corresponding Tafel slopes are 95.37 and 63.17 mV dec⁻¹, respectively. Density functional theory (DFT) calculations indicate that changing the ratio of the internal alloy can regulate the charge distribution on the surface of the outer graphene layer. In addition, in the case of phosphorus-bridged ternary metal alloy core and nitrogen-doped graphene shell, they synergistically increase the electron density and regulate the energy band structure on the surface of the graphene layer, which results in superior HER activity.