As the effective measures in sequestrating carbon (C) of rice paddies, performance of straw returning (SR) and straw-derived biochar application (BA) on the basis of the same C input in regulating CO2 fluxes in atmosphere-rice plant-paddy soil ecosystem under different irrigation mode was monitored across the whole growth stage. Two irrigation managements (i.e., flooding irrigation (FI) and controlled irrigation (CI)) and three carbon managements (i.e., no carbon treatment (K), SR and BA) were set up in a bucket experiment. CO2 fluxes were measured using chamber technology. CI led to an increase in rice leaf instantaneous water use efficiency (WUEleaf) by enhancing rice photosynthetic rate (A) and reducing rice stomatal conductance to water (gsw). Additionally, both BA and SR showed a significant improvement on soil organic carbon (SOC) and net ecosystem exchange of CO2 (NEE), although they promoted soil respiration (Rs). BA was particularly effective in increasing these two parameters. The study also found significant relationships between Rs, gross primary productivity (GPP) and NEE, suggesting that CO2 emission from paddy soil can promote rice photosynthesis. Both BA and SR enhanced the carbon sink function of paddies and reduced soil net carbon loss in water-saving irrigated paddy fields. These results can inform the development of agricultural management measures to improve the carbon sequestration function of rice field ecosystems and aid in the formulation of emission reduction strategies by the government.