A reasonable design of nickel-based catalysts is key to efficient and sustainable energy conversion. For electrocatalytic materials in alkaline electrolytes, however, atomic-level control of the active sites is essential. Moreover, the well-defined surface structure contributes to a deeper understanding of the catalytic mechanism. Here, we report the loading of defective nickel–cobalt layered double hydroxide nanosheets (Ni2Co-LDH@C) after carbonization of silk. Under the precise regulation of the local coordination environment of the catalytic active site and the presence of defects, Ni2Co-LDH@C can provide an ultra-low overpotential of 164.8 mV for hydrogen evolution reactions (HERs) at 10 mA cm−2, exceeding that of commercial Pt/C catalysts. Density functional theory calculations show that Ni2Co-LDH@C optimizes the adsorption energy of the intermediate and promotes the O-O coupling of the active site in the oxygen evolution reaction. When using Ni2Co-LDH@Cs as cathodes and anodes to achieve overall water splitting, a low voltage of 1.63 V is required to achieve a current density of 10 mA cm−2. As an ideal model, Ni2Co-LDH@C has excellent water splitting properties and has the potential to develop water–alkali electrocatalysts.