Understanding the influence factors of nitrogen (N) use efficiencies (NUEs) in different stages of the food system at the provincial scale is critical to achieving cleaner food production while ensuring food security. Nevertheless, they are not well understood. Here we comprehensively analyzed NUE and its influence factors at different stages of the provincial food system. The results showed that per unit agricultural land N input increased by 5–92% in 27 provinces, during 1990–2010, resulting in a low NUE for the crop system when N input per unit agricultural land exceeded about 400 kg N ha^-1. This situation has brought some positive changes, as N input decreased by 3–271 kg N ha^-1 in 77% of the provinces in 2017, relative to that of 2010, but 10 provinces were still over 450 kg N ha^-1 in 2017. Animal food production is expected to continue to expand because 35% and 68% of provinces’ urban and rural households, respectively, were still below the recommended minimum animal food N consumption recommendation in 2017, posing great challenges for reducing environmental N pollution. An exciting result is that the NUE of the animal system can be improved by increasing the share of animal food contributed by poultry, eggs, milk and fish, to align with the diets recommended by the Chinese Nutrition Society. NUEs of the provincial food systems excluding Inner Mongolia, Xinjiang, Qinghai and Tibet, would increase by 13% if the net imported food N increased by 1 kg capita^-1. Nevertheless, virtual NUE—including N input for imported food in the calculation of NUE—should be considered for accurate comparison of the NUEs of the provincial food systems, especially in highly urbanized areas, while N input for non-food animals should be excluded for accurate evaluation of the NUE in pastoral areas, considering their special production systems and feeding structures.