Artificial humic acid (AHA) is a new exogenous organic material with enormous carbon sequestration potential. However, the effects and mechanisms of applying AHA under different irrigation regimes on carbon sequestration in rice-soil systems still need to be clarified. This study applied carbon isotope labeling technology to analyze the photosynthetic carbon sequestration capacity, the carbon transport capacity of the root, and greenhouse gas emission flux in the rice-soil system under different irrigation regimes and AHA application conditions. The results showed that as the amount of AHA applied increased, the leaf area and chlorophyll concentration gradually increased, the Rubisco activity first increased and then decreased under two irrigation regimes. In alternate wetting and drying irrigation with 300 mg kg-1 AHA treatment (DWI3), the photosynthetic carbon fixation ability was the highest, with Pn, Fv/Fm, and qP increasing by 65.35%, 214.85%, and 43.15% compared to alternate wetting and drying irrigation without applying AHA treatment (DWI0), respectively. Meanwhile, during DWI3 treatment, the organic acid concentration in root exudates, root biomass, root length, root surface area, and root length density were also the highest. In summary, among all treatments in this study, the content of 13C in soil under DWI3 treatment was highest, closely related to the strongest photosynthetic carbon fixation and root transport capacity under this treatment, as well as the lower greenhouse gas emission flux. Therefore, it is recommended to apply 300 mg kg-1 AHA with alternate wetting and drying irrigation for carbon sequestration, water conservation, and sustainable agricultural development.