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The practice of co‐incorporating rice straw and leguminous green manure (such as Chinese milk vetch) into paddy soils has become increasingly popular in the last 10 years, although its effect on soil CH4 emissions and microbial community structure is poorly understood. In this study, data from a 2‐year pot experiment were used to reveal the effects of the co‐incorporation of rice straw and Chinese milk vetch on CH4 emissions and methanogenic and methanotrophic communities in paddy soil. Five treatments were chosen: CK (unamended control), CF (inorganic fertilizer), FM (inorganic fertilizer and Chinese milk vetch, 20 g 10 kg−1 dry soil, 4.5 t ha−1), FR (inorganic fertilizer and rice straw, 20 g 10 kg−1 dry soil, 4.5 t ha−1) and FMR (inorganic fertilizer and Chinese milk vetch and rice straw mixture, 5 + 15 g 10 kg−1 dry soil, 1.125 + 2.375 t ha−1). Overall, the soil CH4 emissions in the 2 years under all residue treatments (104.4–122.8 and 83.3–133.3 g CH4 m−2) were higher than those in CK (57.0 and 20.7 g CH4 m−2) and CF (71.8 and 21.9 g CH4 m−2) treatments. The FMR treatment decreased CH4 emissions when compared with FM and FR, especially in the second year. A higher abundance of methanogens (mcrA gene copies) was found under the plant residue‐treated soils (4.35 × 108 g−1 dry soil on average) and FM increased the abundance of methanotrophs (pmoA gene copies, 2.68 × 106 g−1 dry soil). Application of plant residues changed the methanogenic and methanotrophic community structures in comparison with CF (e.g., markedly increased the populations of Methanobacteriales and Methylomonas and suppressed Methanomicrobiales and Methylobacter populations). Methane emissions were significantly and positively related to the mcrA and pmoA gene copy numbers, as well as the mcrA/pmoA ratio. The partial least squares path model (PLS‐PM) indicated that the rice plant biomass (path coefficient = 0.64), the abundance of methanogens (path coefficient = 0.57) and the community structure of methanotrophs (path coefficient = −0.59) were determinants of CH4 emissions. Among the three residue‐treated soils, FMR showed the lowest CH4 emissions and was associated with a slight decrease in the mcrA/pmoA ratio and a significant increase in the Type I/Type II methanotrophs ratio. Thus, we recommend the co‐incorporation of Chinese milk vetch and rice straw as a sustainable fertilization pattern to improve the growth of rice and minimize CH4 emissions. Highlights: Residue application improves rice productivity (except for FR), soil fertility and CH4 emissions.Co‐incorporation of MV and RS reduces CH4 emissions in comparison with pure MV or RS addition.Residue application changes the community structure of methanogens and methanotrophs.The methanogenic abundance and the methanotrophic community structure determine the CH4 emissions. [ABSTRACT FROM AUTHOR]