Diverse development paths among cities within an urban agglomeration can lead to uneven changes in their agricultural production scale, which reshape the inter-city food supply patterns and the spatiotemporal characteristics of nitrogen (N) pollution from the food system. Here, using Guangdong-Hong Kong-Macao Greater Bay Area of China as a case, we found a substantial decrease in N use efficiency of crop production from 45.2% to 29.3% during 1989-2007, along with a growing level of concentration of food N production in less-urbanized cities. From 1989 to 2018, 12.3% to 42.2% of total N pollution in food production became embedded in inter-city trade, leading to aggregation of N pollution in peripheral cities with relatively low levels of economic development. We suggest that protection and intensification of cropland from urban encroachment, as well as enhancing the economic and technical synergies among cities, can serve the sustainable transition of the food system with coordinated N pollution mitigation.
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