Methane (CH₄) fluxes and their key functional microorganisms in a double-cropping paddy field are affected by long-term fertilizer treatment; thus, it was important to utilize and evaluate different fertilization regimes on rice growth. A manual static chamber-gas chromatography (GC) technique was used to verify the effects of different fertilizer treatments, which included mineral fertilizer alone (MF), rice residues plus mineral fertilizer (RF), 30% organic matter plus 70% mineral fertilizer (LOM), 60% organic matter plus 40% mineral fertilizer (HOM), and a control without fertilizer (CK), on CH₄ emissions from double-cropping paddy fields in subtropical regions of China and on the microbial mechanisms driving them. The results showed that the flux of CH₄ from the HOM, LOM, RF, and MF treatments was higher than that of the CK treatment, and it varied with different fertilizer treatments in the following order:HOM > LOM > RF > MF > CK. Further, CH₄ emissions were significantly greater during the entire growth period for early and late rice in the HOM, LOM, RF, and MF treatments than in the CK treatment (P < 0.05). CH₄ emissions from paddy fields in the HOM, LOM, and RF treatments increased by 105.56%, 72.97%, and 54.17%, respectively, compared with the CK treatment. At the main growth stages of early and late rice, the abundance of methanogens under the different fertilizer treatments ranged from 3.18×10³ cfu/g to 81.07×10³ cfu/g, while that of methanotrophs ranged from 24.82×10³ cfu/g to 379.72×10³ cfu/g. The results indicated that the abundance of the methanogens and methanotrophs were significantly greater in the HOM, LOM, RF, and MF treatments at the main growth stages of early and late rice than they were in the CK treatment. Additionally, the abundance of methanogens and methanotrophs varied under the different fertilizer treatments in the following order:HOM > LOM > RF > MF > CK. Moreover, the abundance of methanogens and methanotrophs was significantly greater in the HOM, LOM, and RF treatments at the main growth stages than they were in the MF or CK treatments. CH₄ emissions were significantly correlated with the abundance of methanogens and methanotrophs during the whole growth period. Our results clearly demonstrated that CH₄ emissions from paddy fields and the abundance of key functional microorganism were promoted by the application of inorganic fertilizer combined with organic manure practices in a double paddy field ecosystem.