Winter-flooded rice paddy field (FR), characterized by water conserved in the field during the fallow period, is a typical cropping system in southwest China, leading to considerable methane (CH) emissions. The effect of nitrogen (N) fertilization on CH emissions during rice-growing seasons is well studied in FR, further studies covering N fertilizer applied in the rice-growing seasons affects CH emissions during the subsequent fallow period is needed. Therefore, a field experiment was conducted in an FR of Sichuan province, China, with conventional N fertilized (CN) and N unfertilized (NN) treatments. The cumulative CH emission from CN treatment during the rice-growing season and the subsequent fallow period was 389 ± 29.4 and 158 ± 31.2 kg C ha, which were increased by 29.5% and 395% in comparison with the NN treatment, indicting N applied during the rice growing-season significantly facilitated CH emission during the subsequent fallow period. During the rice-growing season, higher CH emission from CN treatment could be attributed to elevated soil dissolved organic carbon (DOC) content that might have provided sufficient substrates for CH production. During the fallow period, as compared to NN treatment, higher CH emissions from CN treatment could be explained by greater linear regression slopes between CH fluxes, soil temperature and DOC to dissolved inorganic N (DIN) (DOC/DIN) ratio. Moreover, the structural equation model (SEM) described that the soil temperature exhibited the most significant effects on CH emissions for both treatments during the rice-growing season and subsequent fallow period. These findings are a major step forward to showing that N fertilizer applied in the rice-growing season could also affect CH emission during the subsequent fallow period, accompanying other soil parameters controlling CH emission.