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Methanotrophs contribute significantly to methane consumption in paddy ecosystems. Currently, the biogeographical distribution and regulation of methanotrophs in Chinese paddy soils remain poorly understood. Here, we investigated the activity, abundance and community structure of methanotrophs in paddy soils from different geographical regions and three climate zones across China, with a total of 20 sampling sites. The results showed that the methanotrophic activity and pmoA gene abundance varied from 0.67 to 2.23 μmol CH 4 g À1 (dry soil) h À1 and 1.39 Â 10 5 to 1.03 Â 10 7 copies g À1 dry soil, respectively, and the methanotrophic communities were dominated by Methylocystis (type II). Heterogeneously distributed methanotrophic communities were observed among different climate zones characterised by a significant variation of the relative abundance of Methylococcus (type I). Furthermore, high and intermediate rates of nitrogen (N) fertilisation showed a significantly lower methanotrophic activity than the low rates of N fertilisation. However, no significant variation of methanotrophic abundance or community composition was observed among different N fertilisation levels. In addition, the soil ammonium content, water content, clay content, salinity, pH, mean annual precipitation and mean annual temperature was identified as the key factors affecting the activity, abundance and community composition of methanotrophs. Overall, our results showed the biogeographical distribution of methanotrophs in Chinese paddy soils, which can be largely influenced by climate conditions, N fertilisation rates and soil physiochemical properties. Highlights• Activity and abundance of methanotrophs varied greatly across Chinese paddy fields.• Methanotrophic community varied substantially across different climate zones.• Higher rates of N fertilization could decrease methanotrophic activity.• Soil properties (like NH 4 + , pH and moisture) significantly affected methanotrophs.