Biochar amendment can reduce CH4 emissions from paddy soils. However, little is known about how the soil microbial communities associated with paddy soil CH4 emissions respond to biochar aging after biochar amendment. In this study, we examined the effects of biochar on CH4 emissions, soil properties, and abundance/ community composition of methanogens and methanotrophs in a double rice cropping system from 2012 to 2016. Straw-derived biochar was applied once in 2012 at 24 and 48 t ha−1. Biochar application decreased the annual CH4 emissions by 20–51%. Biochar increased the abundances of both methanogens and methanotrophs, with a larger increase of methanotrophs than methanogens in the first year, mainly caused by the increases in soil dissolved organic carbon, NH4 +-N, and porosity. Biochar suppressed the abundance of methanogens and had little effect on the methanotrophs in the following three years, probably due to the increased soil porosity. Eventually, the ratios of abundance of methanogens to methanotrophs decreased by 11–31% in each of the four years and were positively correlated to CH4 emissions. Biochar addition increased the relative abundances of Methanocella and Methanospirillum and reduced those of Methanoregula and Methanosaeta for methanogens, while it increased the proportion of the basophilic methanotrophs Methylomicrobium and decreased that of Methylocaldum in the growing season 2014. Our results demonstrate that biochar aging greatly alters the responses of abundances and community compositions of soil methanogens and methanotrophs to biochar addition. The reduction of CH4 emissions owing to biochar in the long run was probably mainly due to the lesser suppression of abundance and activity of methanotrophs compared with methanogens.