Consumption of nitrogen in food forms an important part of the internal flow of nutrients within human settlements. Spatiotemporal variation in the environmental emissions of nitrogen from food consumption vary considerably between the city and countryside because of the dual economic structure of urban and rural areas. In this study, we used substance flow analysis to simulate the metabolism of nitrogen and constructed a set of models to calculate the quantity of environmental emissions from the consumption of nitrogen in food. The models focused on the different levels of resource recycling of the product after metabolism to determine the trends in environmental emissions of nitrogen from food consumption and the differences between urban and rural areas. The results indicated there was a substantial difference between trends in urban and rural environmental emissions of nitrogen consumed in food from 1993 to 2012. The roles of consumed nitrogen in urban and rural areas, which consisted of the environmental loads in water, soil, and the atmosphere, varied from each other. In terms of water nitrogen loads from food consumption, nitrogen in rural water played a dominant role. However, the difference in nitrogen emissions in water between the city and countryside was gradually decreasing. Regarding soil nitrogen environmental loads from food consumption, nitrogen in the urban soil was the dominant factor. Prior to 2010, the rural atmospheric nitrogen emission was the main factor that influenced the national level of atmospheric nitrogen emissions because of food consumption. Nevertheless, after 2010, the quantity of urban atmospheric nitrogen emissions exceeded that of rural areas, and became the leading factor of the national level of atmospheric nitrogen emissions. Additionally, correlation analysis was adopted to determine whether a positive correlation existed between per capita disposable income and per capita urban resident environmental emissions of nitrogen from food consumption. In addition, the per capita rural resident environmental emissions of nitrogen from food consumption was negatively correlated to the food price index. Based on scenario forecast analysis (SFA), we found that the growth of future national levels of per capita nitrogen emissions from food consumption would be faster than the current trend because of the acceleration of urbanization in China.