Understanding the structural reconstruction of Ni-based materials under electro-reduction conditions and identifying the real active species in the alkaline hydrogen evolution reaction (HER) are significant for developing low-cost and efficient electrocatalysts. Moreover, the role of surface-adsorbed ions has not been fully elucidated after electrochemical reconstruction and severe leaching. Herein, taking (Ni₁₂(OH)₆(SeO₃)₈)(OH)₂ crystal as a pre-catalyst, multiple in situ and ex situ techniques verify that (Ni₁₂(OH)₆(SeO₃)₈)(OH)₂ is destroyed rapidly in the alkaline HER process and reconstructs into metallic Ni, followed by spontaneous surface hydroxylation, ultimately transforming into a Ni/Ni(OH)₂ heterostructure decorated with a small amount of selenite (SeO₃²⁻). The resulting material exhibits a low overpotential of 35 mV for HER at −10 mA cm⁻² in 1 M KOH and can be operated at −300 mA cm⁻² for 120 h without noticeable attenuation, outperforming most non-noble metal electrocatalysts. Theoretical calculations further prove that the surface-adsorbed SeO₃²⁻ can regulate the electronic states of Ni sites, reduce the energy barrier of H₂O-dissociation, and optimize the hydrogen adsorption free energy. These findings provide insight into the structural transformation mechanism and active species of electrode materials during the alkaline HER process.