•CH4 emissions decreased during the rice-growing seasons after the conversion of RF to RW.•The Q10 of CH4 emissions was higher for RW-CN than that for RF-CN.•The soil DOC positively affected CH4 emissions in both RF-CN and RW-CN treatmnets, while the soil DIN negatively affected CH4 emissions. To our knowledge, the conversion of winter flooded rice paddy (RF) to rice-wheat rotation (RW) has markedly decreased methane (CH4) emissions during the wheat-growing seasons. However, the effects of this conversion on CH4 emissions during the rice-growing seasons are unclear. To determine CH4 emissions during the rice-growing season and associated environmental factors under RF and RW systems, a split-plot design experiment was conducted in three RF fields in hilly areas of Sichuan province, China. One-half of each field was converted to RW, and the other half remained RF. Each plot of RW and RF was further divided into four subplots: three subplots for conventional nitrogen fertilization treatment (RW-CN and RF-CN) and one for unfertilized treatment (RW-NN and RF-NN). The study showed that the cumulative CH4 emissions from RW-CN during the rice-growing seasons were 192.77 ± 11.36 and 302.07 ± 28.34 kg C ha−1 in 2013 and 2014, respectively, which were decreased by 26.8% and 24.3% as compared to that from RF-CN. While for RW-NN, the cumulative CH4 emissions decreased by 54.1% and 24.0% as compared to that from RF-NN (372.49 ± 67.05 and 300.53 ± 13.49 kg C ha−1 in 2013 and 2014, respectively, P < 0.05). A higher Q10 (soil temperature sensitivity coefficient) of CH4 emissions during the whole experiment period was observed for RW-CN (6.69) than that for RF-CN (4.48). With rising soil temperature during the rice-growing seasons, the CH4 emissions for RW-CN escalated more rapidly than that for RF-CN. As expected, a positive correlation between CH4 fluxes and soil dissolved organic carbon (DOC) for both RF-CN and RW-CN was observed and DOC in RF-CN during the rice-growing seasons were higher than RW-CN. The soil dissolved inorganic nitrogen (DIN) was negatively correlated to CH4 emissions as the soil temperature ranged 22℃– 28℃. Moreover, rice yields in the RF-CN and RW-CN treatments were similar in both years of 2013 and 2014. These findings suggested that CH4 emissions were primarily controlled by soil environment, which was affected by water and fertilizer managements. The implication of this study is that the decreased CH4 emissions and increased crop yields could be achieved by conversion management from RF to RW.