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Breeding high-yielding rice cultivars through increasing biomass is a key strategy to meet rising global food demands. Yet, increasing rice growth can stimulate methane (CH ) emissions, exacerbating global climate change, as rice cultivation is a major source of this powerful greenhouse gas. Here, we show in a series of experiments that high-yielding rice cultivars actually reduce CH emissions from typical paddy soils. Averaged across 33 rice cultivars, a biomass increase of 10% resulted in a 10.3% decrease in CH emissions in a soil with a high carbon (C) content. Compared to a low-yielding cultivar, a high-yielding cultivar significantly increased root porosity and the abundance of methane-consuming microorganisms, suggesting that the larger and more porous root systems of high-yielding cultivars facilitated CH oxidation by promoting O transport to soils. Our results were further supported by a meta-analysis, showing that high-yielding rice cultivars strongly decrease CH emissions from paddy soils with high organic C contents. Based on our results, increasing rice biomass by 10% could reduce annual CH emissions from Chinese rice agriculture by 7.1%. Our findings suggest that modern rice breeding strategies for high-yielding cultivars can substantially mitigate paddy CH emission in China and other rice growing regions.