Heteroatom doping is regarded as a promising method for controlling the optoelectronic properties of carbon nanodots (CNDs), notably their fluorescence and antioxidation activities. In this study, phosphorous (P) and boron (B) are doped at different quantities in the CNDs’ structures to investigate their effects on the optical and antioxidation properties. Both the dopants can enhance light absorption and fluorescence, yet via different approaches. After doping, the UV–vis absorption of high P%-CNDs demonstrated a slight blue shift (348–345 nm), while the high B%-CNDs showed a minor red shift (348–351 nm), respectively. The fluorescence emission wavelength of doped CNDs changes marginally while the intensity increases significantly. Structural and composition characterizations show elevated levels of C═O on the surface of high P%-CND compared to low P%-CNDs. In B-doped CNDs, more NO₃^– functional groups and O–C═O bonds and fewer C–C bonds form at the surface of high B%-CNDs compared to the low B%-CNDs. A radical scavenging study using 2,2-diphenyl-1-picrylhydrazyl (DPPH) was carried out for all CNDs. It was found that the high B%-CNDs exhibited the highest scavenging capacity. The effects of the atomic properties of dopants and the resulting structures of CNDs, including atomic radius, electronegativity, and bond lengths with carbon, on the optoelectronic property and antioxidative reactions of CNDs are comprehensively discussed. It suggests that the effect of P-doping has a major impact on the carbogenic core structure of the CNDs, while the B-doping mainly impacts the surface functionalities.