Using the free-air CO2 enrichment (FACE) techniques, we carried out a 3-year mono-factorial experiment in temperate paddy rice fields of Japan (1998–2000) and a 3-year multifactorial experiment in subtropical paddy rice fields in the Yangtze River delta in China (2001–2003), to investigate the methane (CH4) emissions in response to an elevated atmospheric CO2 concentration (200±40 mmol mol−1 higher than that in the ambient atmosphere). No significant effect of the elevated CO2 upon seasonal accumulative CH4 emissions was observed in the first rice season, but significant stimulatory effects (CH4 increase ranging from 38% to 188%, with a mean of 88%) were observed in the second and third rice seasons in the fields with or without organic matter addition. The stimulatory effects of the elevated CO2 upon seasonal accumulative CH4 emissions were negatively correlated with the addition rates of decomposable organic carbon (P<0.05), but positively with the rates of nitrogen fertilizers applied in either the current rice season (P<0.05) or the whole year (P<0.01). Six mechanisms were proposed to explain collectively the observations. Soil nitrogen availability was identified as an important regulator. The effect of soil nitrogen availability on the observed relation between elevated CO2 and CH4 emission can be explained by (a) modifying the C/N ratio of the plant residues formed in the previous growing season(s); (b) changing the inhibitory effect of high C/N ratio on plant residue decomposition in the current growing season; and (c) altering the stimulatory effects of CO2 enrichment upon plant growth, as well as nitrogen uptake in the current growing season. This study implies that the concurrent enrichment of reactive nitrogen in the global ecosystems may accelerate the increase of atmospheric methane by initiating a stimulatory effect of the ongoing dramatic atmospheric CO2 enrichment upon methane emissions from nitrogen-poor paddy rice ecosystems and further amplifying the existing stimulatory effect in nitrogen-rich paddy rice ecosystems.