Abstract:The planting experiment was conducted from 2020 to 2021 in the lysimeters at Jiangning District of Nanjing City to investigate the effects of farmland water level and nitrogen fertilization regulations on winter wheat growth, yield, grain quality, water and nitrogen utilization, nitrogen and phosphorus load after the winter wheat suffered from waterlogging during the jointing and booting stage. Winter wheat variety “Yangmai 25” was chosen as the experimental material, after the winter wheat suffered from waterlogging during the jointing and booting stage, three high, middle and low farmland water level (the farmland water level down to -40cm, -60cm, -80cm in 3 days after the 1 day waterlogging) and three low, middle and high nitrogen application rates (160kg/hm2, 190kg/hm2, 220kg/hm2), as well as a control group with non-waterlogging and the nitrogen of 190kg/hm2 were set in the experiment. The results indicated that the winter wheat plant height, aboveground dry matter, yield, water use efficiency,grain crude protein content and grain lysine content were gradually increased with the decrease of farmland water level and nitrogen application rate. Partial factor productivity of nitrogen was increased gradually with the decrease of farmland water level, while decreased with the increase of nitrogen application rate. The total nitrogen, total phosphorus, and other pollutant loads were increased gradually with the decrease of farmland water level. Compared with the control treatment, the increase of nitrogen fertilizer (220kg/hm2) could alleviate the effect of waterlogging stress, and promote the increase of winter wheat aboveground dry matter and yield by 4.76%~23.81% and 2.75%~9.19%, respectively. The reduction of nitrogen fertilizer (160kg/hm2) made the winter wheat yield at the medium and high farmland water level decreased by 2.20 % and 14.00%, respectively, and the corresponding water use efficiency was decreased by 4.55% and 9.74%, respectively. The low farmland water level could decrease the yield reduction effect due to the nitrogen reduction, which increased the yield and nitrogen partial factor productivity of winter wheat by 3.98% and 23.49%, respectively.The higher the farmland water level was, the greater the comprehensive waterlogging degree during the water control period was, and the lower the yield was.In addition, short-term waterlogging had a positive effect on increasing the crude protein content of grains, as the crude protein content of each treatment was increased by 11.50%~20.21% compared with that of the control treatment. Aiming at high yield, high efficiency, pollution reduction and quality improvement,it was recommended that the farmland water level should be lowered to -80cm in 3 days after the winter wheat suffered from waterlogging with 5cm water layer for 1day at winter wheat jointing and booting stage, and the nitrogen application rate should be 220kg/hm2. The research results can provide a theoretical basis for the winter wheat planting and waterlogging disasters restoration in southern China and similar waterloggingprone agricultural areas.