Modification of a photocatalyst with single-atom noble metals can improve its activity while a remaining challenge is the stabilization of single atoms. As a proof of concept, g-C3N4 with desired amount of carbon defects was fabricated to manipulate the distribution of single-atom Pd by taking advantage of its affinity with carbon vacancy-resulted nitrogen atoms. The single-atom Pd was produced by photo-reduction, preferentially located on the carbon vacancy sites as supported by HAADF-STEM and XAFS analyses. As obtained photocatalyst showed high and stable photocatalytic activity in NO conversion; its activity is about 4.4 times higher than that of the pristine g-C3N4. The improved photoactivity was attributed to the preferential separation and transportation of the photo-generated charge carriers due to the introduction of single-atom Pd as evidenced by UV–vis, static and time-resolved photoluminescence spectroscopic analyses. The present work underlines the impetus of surface defect chemistry in the fabrication of single-atom catalysts.