Hydrogen release through water splitting is essential for reducing carbon emissions and promoting the hydrogen economy. One of the crucial challenges for industrial applications of water electrolysis is the manufacture of electrocatalysts which can reduce the kinetic energy barrier of the hydrogen evolution reaction (HER). Loading transition metal (TM) nanoparticles (NPs) or single atoms (SAs) into heteroatom-doped carbon materials (HCMs) is an effective method to improve electrochemical activity and stability. To this end, we synthesized N-doped porous carbon (NC) encapsulated Co NPs and isolated Co SA nanocatalysts (denoted as Co NPs@SAs-NC) using metal-organic frameworks (MOFs) as sacrificial precursors. The Co NPs@SAs-NC nanocatalysts displayed outstanding HER activity with a 110 mV overpotential in 1 M KOH, 47 mV overpotential in 0.5 M H₂SO₄ and 171 mV in 0.5 M phosphate-buffered saline (PBS) to reach a current density of 10 mA·cm⁻². In addition, the mechanism of the synergistic effect of Co NPs, Co SAs and N species was investigated in-depth using in situ shielding experiments and density functional theory (DFT) calculations.