This study provided an insight into a complete green house gases(GHG) accounting of global warming potential(GWP) as affected by water regime in typical double rice-cropping system with crop residue returning. The three water treatments included continuous flooding (F), flooding-midseason drainage-reflooding (F-D-F) and flooding-midseason drainage-reflooding-moist intermittent irrigation (F-D-F-M) in rice growing seasons. Methane and N_2O fluxes were measured using static chamber method. The results showed that annual CH_4 emissions ranged from 208.3 kg/hm~2 for the F-D-F-M plots to 678.2 kg/hm~2 for the F plots, being 60.6%-71.7% from late-rice season. The CH_4 emission was significantly reduced by midseason drainage and intermittent irrigation in comparison with continuous flooding. Annual N_2O emission was 4.75-8.19 kg/hm~2 in the double rice-cropping system. Compared with the F plots, the N_2O emission slightly reduced in the F-D-F plots, while it was remarkably increased in the F-D-F-M plots. Among treatments, the grain yields of early-rice and late-rice were 7.76-8.02 t/hm~2 and 7.22-8.69 t/hm~2, respectively. The GWP ranged from 7648.8 kg/hm~2 for the F-D-F-M plots to 18471.8 kg/hm~2 for the F plots in double rice-cropping system with crop residue returning. The GWP ranged from 0.48 kg/kg to 1.12 kg/kg, significantly reduced for the F-D-F and F-D-F-M plots as compared to F plots. Therefore, agricultural economic viability and GHGs mitigation can be simultaneously achieved by midseason drainage and intermittent irrigation instead of continuous waterlogging in the double rice-cropping system with crop residue returing.