Ratoon rice can improve rice yield by increasing the multiple cropping index in China. However, the greenhouse gas (CH4 and N2O) emission characteristics from ratoon rice fields and the cultivation methods to reduce CH4 and N2O emissions are rarely reported. This study first conducted the analysis of genotype differences in greenhouse gas emission fluxes using five strong ratoon ability rice varieties in 2020. Second, water management methods, including alternating the wet–dry irrigation (AWD) pattern and conventional flooding irrigation (CF) during the main season, were carried out in 2021. CH4 and N2O emission flux, agronomic traits, and rice yield during both main and ratoon seasons were investigated. The results showed that the CH4 emission flux during the main and ratoon seasons was 157.05–470.73 kg·ha–1 and 31.03–84.38 kg·ha–1, respectively, and the total N2O emission flux was 0.13–0.94 kg·ha–1 in the ratoon rice system over the two seasons (RRSTS). Compared with the main season, the CH4 emission flux during the ratoon season was significantly reduced, thus decreasing the greenhouse gas global warming potential (GWP) and greenhouse gas emission intensity (GHGI) in the ratoon rice system. Cliangyouhuazhan (CLYHZ) showed a high yield, and the lowest GWP and GHGI values among the five rice varieties in RRSTS. Compared with CF, the AWD pattern reduced the CH4 emission flux during the main and ratoon seasons by 67.4–95.3 kg·ha–1 and 1.7–5.1 kg·ha–1, respectively, but increased the N2O emission flux by 0.1–0.6 kg·ha–1 during the RRSTS. Further, compared with CF, the AWD pattern had a declined GWP by 14.3–19.4% and GHGI by 30.3–34.3% during the RRSTS, which was attributed to the significant reduction in GWP and GHGI during the main season. The AWD pattern significantly increased rice yield by 21.9–22.9% during the RRSTS, especially for YX203. Correlation analysis showed that CH4, GWP, and GHGI exhibited significant negative correlations with spikelet number per m2 and the harvest index during the main and ratoon seasons. Collectively, selecting the high-yield, low-emission variety CLYHZ could significantly reduce greenhouse gas emissions from ratoon rice while maintaining a high yield. The AWD pattern could reduce total CH4 emission during the main season, reducing the GWP and GHGI while increasing the ratoon rice system yield. It could be concluded that a variety of CLYHZ and AWD patterns are worthy of promotion and application to decrease greenhouse gas emissions in the ratoon rice area in the upper reaches of Yangtze River, China.
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