Significance The biogeochemical cycle of phosphorus (P) has been massively altered in China, challenging its food security and causing eutrophication of freshwaters. This study shows, for the first time to our knowledge, how P cycling in China was intensified in the past four centuries to sustain the increasing population and its demand for animal protein. Our analysis also reveals the spatial disparity of its concomitant eutrophication impact. The findings advance the knowledge base needed for closing the P cycle to sustain future food production and maintain healthy rivers, lakes, and oceans.