Abstract: Experiments were carried out on the experiment farm of Anhui Agricultural university with pot culture from 2005 to 2007. Effects of waterlogging at filling stage on N、P、K nutrition metabolism and yield were studied applying simulation waterlogging method. The results showed that waterlogging at filling stage significantly influenced N and P and K nutrition absorption and transportation and distribution of different cultivars ,decreased N and P and K nutrition assimilation content of root system and stem and sheath and green leaf and grain, reduced N and P nutrition distribution ratio of root system and function leaf and increased N and P nutrition distribution ratio of stem and sheath and grain, and less influenced K nutrition distribution ratio of different organs. So applying rich P and K fertilizer at basal fertilizer and rapidly available N fertilizer form jointing stage to booting stage and it is very important that to reduce waterlogging injury and to increase grains yield of waterlogging wheat.