Photocatalytic hydrogen evolution is an attractive field for future environment-friendly energy. However, fast recombination of photogenerated charges severely inhibits hydrogen efficiency. Single-atom cocatalysts such as Pt have emerged as an effective method to enhance the photocatalytic activity by introduction of active sites and boosting charge separation with low-coordination environment. Herein, we demonstrated a new strategy to develop a highly active Pd single atom in carbon-deficient g-C3N4 with a unique coordination. The single-atom Pd–N3 sites constructed by oil bath heating and photoreduction process were confirmed by HADDF-STEM and XPS measurements. Introduction of single-atom Pd greatly improved the separation and transportation of charge carriers, leading to a longer lifespan for consequent reactions. The obtained single-atom Pd loaded on the carbon-deficient g–C3N4 showed excellent photocatalytic activity in hydrogen production with about 24 and 4 times higher activity than that of g–C3N4 and nano-sized Pd on the same support, respectively. This work provides a new insight on the design of single-atom catalyst.