Taking the China rice/wheat FACE (Free-Air Carbon Dioxide Enrichment) as a platform, this paper studied the effects of elevated CO2 on the NH4(+)-N and NO3(-)-N contents at different depths of paddy soil in rice season. Under elevated CO2, the NH4(+)-N content in plough layer increased at early growth stage but decreased at late growth stage, and the soil NO3(-)-N content at the depths 5, 15, 30, 60, and 90 cm increased by 46.5%, 36.8%, 23.3%, 103.7%, and 42.7%, respectively, with a significant increase occurred at the depths 60 cm (P < 0.01) and 90 cm (P < 0.05), compared with the control.