Food nitrogen (N), which includes animal-food (AN) and plant-food N (PN), has been driven by population growth (PG), dietary changes associated with income growth (DC) and rural-urban migration (M) over the past three decades, and these changes combined with their N cost, have caused some effect on N use in China's food system. Although there is an increasing literature on food N and its environmental impacts in China, the relative magnitude of these driving forces are not well understood. Here we first quantify the differences in per capita AN and PN consumption in urban and rural areas and their impacts on N input to the food system during 1990–2012, and then quantify the relative contributions of DC, PG and M in the overall N change during this period. Our results show that a resident registered as living in city required 0.5 kg more AN yr^{− 1} and 0.5 kg less PN yr^{− 1} than one living in a rural area, in 2012. DC, PG and M accounted for 52%, 31% and 17% of the total AN increase, respectively. These three factors caused 46% of the increased N use for food production over the past two decades. Another 54% was mainly caused by the declining in N use efficiencies of the food system. Food-sourced N loss intensity in urban and rural areas were 502 and 162 kg N hm^{− 2} in 2012, a three-fold difference due to the increasing amount and a linear rural-urban flow of N input, and inadequate N recovery via solid waste and wastewater treatment in cities. Our study highlights China is facing higher risks of environmental N pollution with urbanization, because of the high demand for AN and higher food-sourced N loss intensity in urban than in rural areas.