To evaluate variations of CO2 and CH4 emissions from two FACE (free-air CO2 enrichment, F) soils and one ambient (A) soil three years after rice wheat rotation FACE treatment, laboratory incubation experiments with laboratory and elevated CO2 concentration (1000 μl L-1) were carried out under flooded conditions and at 25℃. Results show that soil organic carbon is increased by 11% after exposed to FACE treatment for three years. The results indicates that the cumulative CO2 emissions from FACE soils are 35% and 22% higher than that from the ambient soils, while the cumulative CH4 emissions from FACE soils are 2.6 and 2.3 times of that from the ambient soils. Thus, there is a larger ratio of the cumulative emissions of CH4 to CO2 in the soil F. Elevated CO2 concentration during the incubation stimulates the cumulative CO2 emission significantly, but its stimulation on CH4 emission is not statistically significant. The results indicate that elevated atmospheric CO2 concentration stimulates the turnover rates of soil organic matter with a net increase in soil organic matter content and alters the CH4/CO2 ratio.