A pot experiment was conducted to investigate CH4 emissions from a sandy paddy soil as influenced by rice cultivars and atmospheric CO2 elevation. The experiment with two CO2 levels, 370 μL L−1 (ambient) and 570 μL L−1 (elevated), was performed in a climatron, located at the National Institute for Agro-Environmental Sciences, Tsukuba, Japan. Four rice cultivars were tested in this experiment, including IR65598, IR72, Dular and Koshihikari. Tiller number, root length and grain yield were clearly larger under elevated CO2 than under ambient CO2. IR72 and Dular showed significantly higher tiller number, root length and grain yield than Koshihikari and IR65598. Average daily CH4 fluxes under elevated CO2 were significantly larger by 10.9–23.8% than those under ambient CO2, and varied with the cultivars in the sequence Dular ≧ IR72>IR65598 ≧ Koshihikari. Dissolved organic C (DOC) content in the soil was obviously higher under elevated CO2 than under ambient CO2 and differed among the cultivars, in the sequence IR72>Dular>Koshihikari>IR65598. The differences in average daily CH4 fluxes between CO2 levels and among the cultivars were related to different root exudation as DOC content, root length and tiller number. This study indicated that Koshihikari should be a potential cultivar for mitigating CH4 emission and simultaneously keeping stable grain yield, because this cultivar emitted lowest CH4 emission and produced medium grain yield.