Field experiment were conducted in the hilly area of Central Sichuan to investigate the effects of altering rice-flooded-fallow ( RF) to rice-wheat rotation ( RW) on the emissions of CH4, CO2 and N2O. Gas fluxes were analyzed by static opaque chamber and gas chromatography techniques. Soil samples were collected to determine dissolved organic carbon and nitrogen concentrations. Soil temperature and moisture were measured at the same time of gas sampling. Results showed that average CH4,CO2( ecosystem respiration ) and N2O fluxes for RW treatment were 0.05, 117.01 mg?m~(-2)?h~(-1) and 77.19 ,respectively, and were 1.43,7.85 mg?m-(-2)?h~(-1) and -0.61 mug?m-(-2)?h~(-1),respectively, for RF treatment. N_2O flux peak was observed after nitrogen fertilizer application from RW, and the N20 direct emission factor for RW was 1.28%. Soil dissolved organic carbon content was significantly correlated with C02 flux (r = 0.342,p < 0.01). Nitrate and dissolved total nitrogen was positively correlated with N20 flux while negatively with CH4 flux. Global warming potentials of three greenhouse gases were 3.03 Mg?hm-2 for RF, which was higher than that for RW ( -1.66 Mg?hm~(-2)). Result of this study proved that converting RF to RW decreased global warming impact of the ecosystem.