Aiming at the problems of reduced winter wheat yield and aggravation of nitrogen leaching pollution caused by the waterlogging in the Middle-Lower Yangtze Plain, China, a two-year field experiment with three farmland water levels (W40, W60, W80) and three nitrogen application rates (N150, N225, N300) as well as a non-waterlogged treatment (CK) was carried out, to investigate the coupling effects of farmland water level and nitrogen application rate on the plant growth, grain yield, crop water productivity (WPC) and nitrogen load with waterlogging conditions. Three man-made waterlogging events were applied at winter wheat jointing-booting stage, heading-flowering stage and grain filling stage, respectively. The results indicated that with the farmland water level decreased from −40 cm to −60 cm and the nitrogen application rate increased from 150 kg∙ha−1 to 225 kg∙ha−1, the plant height, aboveground dry matter, leaf area index, spike length, grain yield, effective panicles, grain number per ear, 1000-grain weight and WPC in the waterlogging field increased significantly. However, since the nitrogen application rate exceeded 225 kg∙ha−1 and farmland water level lowered more than −60 cm, the favorable effects of nitrogen application rate and farmland water level for winter wheat growth and production reduced. Additionally, both the nitrogen load and partial factor productivity of nitrogen (PFPN) increased with the decline of farmland water level, while the nitrogen load increased and the PFPN decreased with the increasing nitrogen application rate. The raise of nitrogen rate from 150 kg∙ha−1 to 225 kg∙ha−1 was beneficial to plant growth, however, the increase of nitrogen application resulted in the decrease of PFPN and increase of drainage nitrogen loads. Compared with the water farmland water level of −40 cm and nitrogen application rate of 150 kg∙ha−1, the increase of nitrogen application rate and the decrease of farmland water level in the range of 50%-100% resulted in yield raise by 5.78%-32.29% approximately and the increase of nitrogen load by 36.20%-178.44% approximately. The comprehensive evaluation with TOPSIS-Entropy method for plant growth, grain yield, WPC, PFPN and nitrogen loads suggested that, the appropriate nitrogen application rate for winter wheat in the waterlogging areas of Middle-Lower Yangtze Plain in China was 225 kg∙ha−1, and the proper farmland water level was lowering to −80 cm in wet year and −60 cm in dry year within 3 days after waterlogging.