N‐doped carbon‐encapsulated transition metal selenides (TMSs) have garnered increasing attention as promising electrocatalysts for hydrogen evolution reaction (HER). Accurately regulating the electronic structure of these nanohybrids to reveal the underlying mechanism for enhanced HER performances is still challenging and thus requires deep excavation. Herein, a series of pomegranate‐like NixSey@NC core–shell nanohybrids (including Ni0.85Se @ NC, NiSe2@NC, and NiSe@NC) through controllable selenization of a Ni‐MOF precursor is reported. The component of the nanohybrids can be fine‐tuned by tailoring the selenization temperature and feed ratio, through which the electronic structure can be synchronously regulated. Among these nanohybrids, the Ni0.85Se @ NC exhibits the optimum pH‐universal HER performance with overpotentials of 131, 135, and 183 mV in 0.5 m H2SO4, 1.0 m KOH, and 1.0 m PBS, respectively, at 10 mA cm−2, which are attributed to the increased partial density of state at the Fermi level and effective van der Waals interactions between Ni0.85Se and NC matrix explained by density functional theory calculations.