In this study, using membrane inlet mass spectrometry (MIMS), the impacts of different rates of N fertilizer application on denitrification, as well as ammonia (NH3) volatilization, were investigated over two rice-growing seasons in the Taihu Lake region of China. In N300 treatment, N loss through denitrification and NH₃ volatilization were N 54.8 kg/hm² and 54.0 kg/hm² per year, respectively, and were 18.3% and 18.0% of N fertilizer application, respectively. The amount of N loss through denitrification and NH₃ volatilization were increased as the N fertilizer application increasing, and were significantly affected by NH₄⁺-N, NO₃^--N, DOC and pH of surface water. In N270 treatment, compared with N300, the rate of N fertilizer application was reduced by 10%, but the rice yield approximately increased by 5.5%, N losses through denitrification and NH₃ volatilization were decreased by 1.1% and 3.1%, respectively, and agronomic nitrogen efficiency (NUE) was increased by 5.5%. In N375 treatment, compared with N300, NUE was increased due to increased grain yield, but the amount of N losses through NH₃ volatilization and denitrification was also the largest. Thus, the aim to reduce N fertilizer application and increase rice yield and NUE could be achieved through integrated soil-crop system management (ISSM).