Human activity greatly influences nitrogen (N) pollution in urbanized and adjacent areas. We comprehensively studied the N cycling in an urban-rural complex system, the Greater Hangzhou Area (GHA) in southeastern China. Our results indicated that subsurface N accumulation doubled, riverine N export tripled and atmospheric N pollutants increased 2.5 times within the GHA from 1980-2004. Agriculture was the largest N pollution source to air and water before 2000, whereas industry and human living gradually became the primary N pollution sources with the socioeconomic development. Based on the sensitivity analysis, we developed a scenario analysis to quantify the effects of technology and policy on environmental N dynamics. The fertilization reduction scenario suggested that the groundwater N pollution could decrease by 17% with less than a 5% reduction in crop production; the N effluent standard revision scenario led to a surface water N pollution reduction of 45%; the constructed wetlands implementation scenario could reduce surface water pollution by 43%-64%. Lastly, the technological improvement scenario mitigated atmospheric N pollution by 65%. Technologies play a key role in atmospheric N pollution control, policies mainly contribute to groundwater N pollution control, while technology and policy both work on surface water N mitigation within an urban-rural complex.