The development of inexpensive, highly active, and stable non-precious metal catalysts is the key to efficient H2 production by the electrolysis of water. Based on initial theoretical predictions, we report the design and synthesis of N-doped, defect-containing, carbon-dots (CDs)-loaded molybdenum phosphide (MoP/CDs) nanoparticles using CDs with different N contents. This optimized composite material performed outstandingly in the hydrogen evolution reaction (HER), with an overpotential of 70 mV at a current density of 10 mA cm−2 with a 1.0 M KOH electrolyte. N doping changed the electronic arrangement around the reaction site, promoting the adsorption of HER intermediates. Increasing the N content further activated the adjacent C atoms to detach due to the more negative C vacancy formation energies resulting in a defect site with lost atoms and changed bond lengths. The introduction of defects increases the number of dangling bonds adjacent to reaction sites and reduces site coordination numbers, changing their electrocatalytic activity. Results show that N-doped and defect-containing MoP/CDs nanoparticles have excellent H2 production performance during the electrolysis of alkaline solution. These findings open a new area of application of heteroatom-doped CDs and provide new ideas for the design of efficient carbon-semiconductor composite HER catalysts.