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Rice paddy has been the main source of anthropogenic methane (CH 4) emissions, with significant variations among rice varieties. 2-Acetyl-1-pyrroline (2-AP) is the key component of the pleasant aroma in fragrant rice. Here, we show that fragrant rice is metabolically active in nitrogen assimilation and exhibits high levels of 2-AP and that CH 4 fluxes at the booting stage and cumulative emissions are 25.5% and 14.8% lower, respectively, in fragrant rice paddies compared with nonfragrant rice paddies. Three precursors involved in 2-AP synthesis—proline, glutamic acid, and ornithine—are identified as crucial nitrogen compounds that significantly promote CH 4 oxidation in the rhizosphere. Augmenting 2-AP synthesis, either through foliar spraying or by utilizing CRISPR-Cas9 technology to generate knockout lines of BETAINE ALDEHYDE DEHYDROGENASE 2 gene, effectively enhances CH 4 oxidation and reduces CH 4 fluxes. Our findings reveal that the 2-AP metabolic pathway coordinates the carbon/nitrogen cycle to improve nitrogen assimilation along with high 2-AP levels and mitigate CH 4 emissions in paddy ecosystems. [Display omitted] • 2-AP metabolism in fragrant rice reduces cumulative CH 4 emissions by 14.8% • Precursors of 2-AP synthesis—Pro, Glu, and Orn—are crucial to CH 4 mitigation • Mutants of BADH2 increase endogenous 2-AP level and reduces CH 4 emissions • Foliar spraying with exogenous 2-AP improves methanotrophy and decreases CH 4 fluxes Chen et al. show that fragrant rice is active in nitrogen assimilation, accompanied by a high level of the aromatic compound 2-acetyl-1-pyrroline (2-AP). The metabolic process of 2-AP and its interaction with rhizosphere microbes effectively enhance CH 4 oxidation and mitigate CH 4 emissions in paddy ecosystems. [ABSTRACT FROM AUTHOR]