Determinations on the CH4 and N2O emissions from phaeozem rice field showed that their emission amount in rice growing season was much lower than any other regions in China. There was trade-off relationship between CH4 and N2O emissions(r = -0.513, P < 0.05). Under the same fertilization, compared with continual irrigation, intermittent irrigation could reduce significantly CH4 emission and increase N2O emission, but the overall warming potential of greenhouse effect was reduced greatly, while rice yield was not affected. Therefore, intermittent irrigation was an effective irrigation measures to reduce greenhouse gas emissions from rice field. In addition, investigations on CH4 and N2O emissions and their related microbial process showed a positive relation between methanogens number and CH4 emission(R2 = 0.82, P < 0.05), and the important relationship between the numbers of nitrifiers and denitrifiers and N2O emissions.