Rice fields contribute substantially to greenhouse gas emissions, and water managements affect this contribution. In this study, a field experiment was designed to examine the effects of irrigation water on yields and greenhouse gas emissions by keeping different depths of standing water(10 cm, 15 cm, and 20 cm) in paddy field from milking to maturity stage of early rice. Compared to traditional water regime(CK), deep standing water improved plant photosynthetic rate, but reduced seed setting rate and 1000-grain weight, resulting in 3.1%~5.7% reduction of rice yields with no significant difference. However, deep standing water treatments increased the cumulative CH_4 emission by 62.7%~113.6%, but decreased the cumulative N_2O emission by 63.1%~84.1%, compared to the control. Significant differences were found among the treatments. The global warming potential(GWP) of CH_4 and N_2O was found to be the highest in the 10 cm depth of standing water. The deeper the standing water, the lower GWPs were observed. Overall, the GWP was 57.2%~96.6% higher in deep standing water than in CK. In conclusion, holding 20 cm depth water in early rice field would benefit late rice cultivation in the double-season rice area of Hunan Province. Further study is necessary on reducing CH_4 emission from deep standing water paddy field.