Nitrogen (N) and phosphorus (P) are essential nutrients for living systems and play a central role in human food systems. While N and P pathways have been investigated individually in the literature, the N-P coupled cycling network has not received sufficient attention. The coupled nature of N and P cycling networks and the importance of their resilience for the future of food and energy systems is of critical importance for sustainable development. In this avenue, we use the material flow and ecological network analysis methods to construct the N-P coupled cycling network in China and evaluate its resilience. The results show that the resilience of China’s N-P coupled cycling network decreased during the 1980–2017 period and, given China’s goal of further carbon neutrality, resilience is expected to continue decreasing throughout the study period (until 2060). Furthermore, under our clean energy scenario, the N-P coupled cycling network will have a very substantial decrease in its resilience, especially in the N layer (by 20%). China’s socio-economic system also suffers the risk of great N emissions to the environment, thus disturbing the N cycle, and amplifying the conflict between energy and food systems given the scarcity of P. Our findings reveal trade-offs and synergies under future anthropogenic nexus scenarios and can equip policymakers to make more informed deliberations on the management of N and P cycling networks in China, e.g., reducing fertilizer use and food waste.