Atomically ordered precious intermetallic nanoparticles have garnered significant attention for diverse applications due to their well-defined surface atomic arrangements and exceptional electronic and geometric properties. However, synthesizing non-precious ordered intermetallics that exhibit high stability under operating conditions remains a formidable challenge, primarily owing to their strong oxyphilicity, highly negative reduction potentials, and low corrosion resistance. In this work, we report a facile yet versatile seed-mediated solid-phase approach for fabricating uniform Ni₃Ga₁ intermetallic nanocubes (NCs) fully encapsulated within N-doped carbon layers (denoted as Ni₃Ga₁@NC-800). Extensive characterization confirms the formation of a unique core–shell architecture, with atomic-resolution structural analysis and X-ray absorption fine structure measurements unequivocally verifying the atomically ordered Ni₃Ga₁ intermetallic phase. The Ni₃Ga₁@NC-800 catalyst demonstrates exceptional performance in the 1,4-hydrogenation of α,β-unsaturated carbonyl compounds, exhibiting both remarkable activity and exclusive selectivity while maintaining high stability over multiple reaction cycles without observable performance decay. Combined experimental and theoretical calculations reveal that the strong interatomic p–d orbital hybridization facilitates electron transfer from Ga to Ni atoms, resulting in electron localization on ordered Ni atoms. This electronic configuration positively influences H₂ activation and optimizes substrate adsorption strength, thereby substantially improving catalytic efficiency. Furthermore, this synthetic strategy proves generalizable, successfully extending to the synthesis of other non-precious ordered Ni₁Sn₁ and Ni₂In₃ intermetallics confined within N-doped carbon matrices.