The resilience of the phosphorus (P) cycling network is critical to ecosystem functioning and human activities. Although P cycling pathways have been previously mapped, a knowledge gap remains in evaluating the P network’s ability to withstand shocks or disturbances. Applying principles of mass balance and ecological network analysis, we examine the network resilience of P cycling in China from 1600 to 2012. The results show that changes in network resilience have shifted from being driven by natural P flows for food production to being driven by industrial P flows for chemical fertilizer production. Urbanization has intensified the one-way journey of P, further deteriorating network resilience. Over 2000–2012, the network resilience of P cycling has decreased by 11% owing to dietary changes towards more animal-based foods. A trade-off between network resilience improvement and increasing food trade is also observed. These findings can support policy decisions for enhanced P cycling network resilience in China.