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Rice paddies are a significant source of atmospheric methane (CH4) threatening global warming. Methane fluxes from rice soils are mediated by both methanogens and methanotrophs, while subject to fertilization regimes. A field experiment was conducted to investigate the response of CH4 emissions, with a close link to methanogenic and methanotrophic communities, to different fertilization strategies over two consecutive rice growing seasons in a paddy field. Four fertilized treatments were established consisting of chemical phosphorous (P) and potassium (K) fertilizer (PK), chemical nitrogen (N) PK fertilizer (NPK), chemical NPK combined with organic manure (NPKM), and organic manure alone (M). Results showed that, relative to chemical PK treatment without N fertilizer input, the application of chemical NPK fertilizer, manure, and their combination significantly increased seasonal mean CH4 emissions by 67.4, 20.4 and 101.2%, respectively. Methane fluxes were significantly and positively (r(2) = 0.75) related to mcrA gene copy numbers and the ratio of mcrA/pmoA, while negatively (r(2) = 0.40) related to pmoA gene copy numbers, which was mainly regulated by the dynamics of water irrigation regime. The abundance of mcrA and pmoA had trade-off relationship over the rice growing season. In comparison with PK fertilization, N fertilized treatments did not alter the seasonal trend of CH4 fluxes, but enhanced the source strength of CH4 emissions through increased mcrA abundances rather than reduced pmoA-dominated methanotrophic CH4 oxidation in rice paddies. In contrast, N fertilization showed no effect on pmoA abundance and associated methanotrophic community in rice paddies. Results highlight that, given the fertilizer-driven balance between methanogenic and methanotrophic communities, fertilization options with either chemical or organic N input stimulated CH4 emissions mainly through improving soil C substrate and methanogenic activities, especially under the combination of chemical and organic N fertilization in rice paddies.