Two non-CO2 greenhouse gas emissions (methane and nitrous oxide) and related environmental factors were measured within rice growing season under five treatments including non-fertilization (CK), balanced fertilization (BF), decreased nitrogen and phosphate 1 (DNP1), decreased nitrogen and phosphate 2 (DNP2) and increased nitrogen and phosphate 1 (INP) in double rice fields of red clay soil in 2009, using the method of static chamber-gas chromatograph techniques. The results showed that the average CH4 emission fluxes for treatments of BF, DNP1, DNP2 and INP were 4.57, 5.42, 4.70 and 4.65 mg x (m2 x h)(-1) during early rice growing period, which increased by 39%, 49%, 41% and 40% compared with non-fertilizer treatment, respectively. The average CH4 emission fluxes in late rice growing season was higher than preseason's. Compared to CK, CH4 emission increased by 11%, 1%, 26% and - 4% in treatments of BF, DNP1, DNP2 and INP within late rice growing season. Applying nitrogen and phosphate enhanced CH4 emission in turning green period for early and late rice. No significant difference was observed between the CH4 emissions of five treatments during early and late rice growing season (p > 0.05). N2O emission was very little during mid-seasonal drainage period. In contrast, N2O emission peaks were observed in period of alternation of wetting and drying after mid-seasonal drainage in this experiment. N2O emission was, on average, equivalent to 0.18% of the nitrogen applied in double rice growing season. Statistically, air temperature, soil Eh and soil moisture (water-filled pore space, WFPS) at 0-10cm depth significantly affected the fluctuations of the seasonal CH4 flux, but no significant correlationship has been found between N2O flux and related environmental factors. CH4 was the dominated greenhouse gas in double rice fields which contributed approximately 90% for the integrated global warming potential of CH4 and N2O released during the rice growing season. Therefore, the mitigation options should focus on how to reduce CH4 emission in local area. The result indicates that BF is a recommended fertilization method for early rice production, and a optimum fertilization for late season can increase rates of nitrogen and phosphate fertilizers on the basis of BF treatment slightly by considering total global warming potential and grain yield. The rates of BF treatment were 150-90-90 kg x hm(-2) N-P2O5-K2O for early rice, and 180-90-135 kg x hm(-2) N-P2O5-K2O for late rice, respectively.