Nitrogen is an important component of protein and essential element for all lives. Anthropogenic changes to both global and regional nitrogen cycling have contributed an adequate supply to industrial and agricultural products since the 20th century. It is also an excessive nitrogen input to water, air and soil, leading to huge ecological pressure and environmental pollutions, such as eutrophication,soil acidification and climate change. Quantifying the pathway of nitrogen throughout the socio-economic system is one of the effective approaches to regulate nitrogen emissions and mitigate or avoid producing environmental pollution. Based on substance flow analysis method,a framework was developed to analyze nitrogen flows in the key producing and consuming processes of socioeconomic system at regional level. A case study for the Middle-Lower Yangtze River Belt was brought out to calculate the amount of environmental emissions in the urban agglomeration. The results showed that the total nitrogen input and output of entire socio-economic system was 993.56 * 10~4 t and 732.84 * 10~4 t in 2011,respectively. The nitrogen input mainly consisted of the industrial nitrogen fixation,animal feed imports and energy consumption; meanwhile,the nitrogen output mainly came from environmental emission. Besides,the total nitrogen output of the whole system emitting to environment in 2011 was about 760.99 * 10~4 t including 47.24% to atmosphere,19.42% to soil surplus and 18.60% to water. The proportions of the six source emissions were 43.83% in the agricultural subsystem,16.59% in the industrial subsystem,16.14% in the urban subsystem,13.96% in the livestock and poultry subsystem,6.08% in the aquaculture subsystem and 3.40% in the rural subsystem. Over-fertilization in agricultural activities, livestock nitrogen emission and its decoupling from agricultural cultivation,low domestic waste treatment percentage high energy consumption and pollution in industries as well as motor vehicle emissions were the main causes for the observed environmental nitrogen loading in this region. Based on above analysis,we emphasized optimizing fertilizer application structure,promoting comprehensive utilization of livestock waste,changing industrial energy consumption,and implementing strict motor vehicle emission regulations.