Straw return (SR) and rice water-saving irrigation (WSI) affect the greenhouse gas emission of paddy fields. However, studies on CO2 exchange between paddy fields and the atmosphere with joint regulation of SR and WSI are few. We conducted a two-year field experiment to investigate the effects of SR on soil respiration and net ecosystem exchange of CO2 (NEE) in paddy fields under controlled irrigation (CI), which is a typical WSI technique. The rice yields, irrigation water use efficiency, seasonal variations in soil respiration, NEE, and soil organic carbon content were measured. Compared with the control (flooding irrigation and traditional chemical fertilizer), a significant increase in rice yield and irrigation water use efficiency in the paddy fields under CI and SR joint management (CS) was observed. CS increased the soil respiration rate during most of the rice growth stage and increased the net CO2 absorption rate before approximately 80 days after transplanting; afterward, the pattern reversed. Total CO2 emissions through soil respiration in CS paddy fields increased by 43.7% and 182% compared with the control in 2014 and 2015, respectively. However, CS also caused an increase in the total net CO2 absorption by 18.1% and 30.1% in these two years, respectively. The acceleration in the consumption and decomposition of soil organic carbon induced by frequent alternate wet–dry cycles of the CI paddy fields increased the soil respiration and decreased the net CO2 absorption. SR promoted soil respiration but also improved rice growth, increasing the net CO2 absorption. The soil organic carbon content of the CS paddy fields after harvesting increased by 23.2% compared with that before transplanting. The present study concluded that joint regulation of WSI and SR is an effective measure for maintaining yield, increasing irrigation water use efficiency, mitigating CO2 emission, and promoting paddy soil fertility.
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