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Abstract Global agricultural trade creates multiple telecoupled flows of nitrogen (N) and phosphorus (P). The flows of physical and virtual nutrients along with trade have discrepant effects on natural resources in different countries. However, existing literature has not quantified or analyzed such effects yet. Here we quantified the physical and virtual N and P flows embedded in the global agricultural trade networks from 1997 to 2016 and elaborated components of the telecoupling framework. The N and P flows both increased continuously and more than 25% of global consumption of nutrients in agricultural products were related to physical nutrient flows, while virtual nutrient flows were equivalent to one-third of the nutrients inputs into global agricultural system. These flows have positive telecoupling effects on saving N and P resources at the global scale. Reducing inefficient trade flows will enhance resource conservation, environmental sustainability in the hyper-globalized world.