The effects of water-saving irrigation on the emissions of greenhouse gases and the prokaryotic communities in rice paddy soils were investigated through a field experiment. In the Water-Saving (WS) irrigation, the water layer was kept at 2~3 cm while it was kept at 6 cm in the Continuousiy Flooding (CF) irrigation. A plot was treated with Intermittently Drainage (ID) that is drained as fine cracks on the floor were seen after transplanting. GHGs emission amounts from WS plots were reduced by 78.1% compared to that from CF plot and by 70.7% compared to that from ID plot, meaning that WS could help contribute to mitigation of the greenhouse gas accumulation in the atmosphere.