The consumption of food, energy, and industrial products in cities results in large quantities of excess nitrogen circulating in socio-ecological systems. However, details about how nitrogen flows and transforms within urban systems are unclear. In this study, we analyzed the nitrogen processes of Beijing considering the influences from human activities and nature under the framework of urban metabolism. Ecological network analysis was used to track the integral (direct + indirect) flows and to compare the contribution of direct and indirect flows at both the scale of each component and of the whole urban system during the period from 1996 to 2012. We found that Atmosphere, Household, and Industry had the most interactions with other nodes in the network. The integral flow from Industry to Atmosphere, which was consistently at 200 Gg, was the largest at five time points; the flow from Household to Sewage treatment grew fastest, and in 2012, increased to 5.9 times its 1996 value; the flow from Industry to Farmland decreased most obviously, and in 2012, it decreased to 12.9% of the value in 1996. Moreover, the indirect effects were dominant for the whole system in Beijing with a ratio of indirect to direct flow equal to 1.2. Surface Water and Forest had the strongest indirect effects maintaining a ratio of almost 2. Meanwhile, exploitation and competition relations were most frequent and their proportions were much larger than the proportion of mutualism relations. Through our results, integral flows were found to identify accurately the crucial process of nitrogen metabolism and our results showed how these ecological relationships influence the urban nitrogen flows within the system.