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Excess inputs of nitrogen (N) and phosphorus (P) are the main contributors of aquatic environmental deterioration. Due to the agricultural and industrial activities in the rapidly urbanized basin, the anthropogenic N and P cycle are significantly different from other regions. In this study, we took the Pearl River Delta as an example and introduced the budget list of N and P in the five survey years, including the net anthropogenic N inputs (NANI) and net anthropogenic P inputs (NAPI). The results revealed that the intensities of NANI and NAPI in this area increased from 2008 to 2010 and then decreased after 2010. The peak values were 21001 kg N km−2yr−1 and 4515 kg P km−2yr−1 for the intensities of NNAI and NAPI, respectively, while the lowest values decreased to 19186 kg N km−2yr−1 and 4103 kg P km−2yr−1 in 2016. The most important contribution of NANI and NAPI sources in this area were net N and P inputs for human food and animal feed with an average contribution of 61.41% and 76.83%, which indicated that large amounts of N and P were introduced into the environment through the food system. This study expanded the knowledge on regional environmental management from human dietary consumption, human life consumption, animal consumption and fertilizer consumption. Its reuse will be put into practice by understanding the driving factors of N and P inputs in each region of the basin, combining the urbanization characteristics. • The mean intensities of NANI and NAPI in the Pearl River Delta basin were higher than that of the mean level in China. • Human food and animal feed inputs comprised more than 60% for NANI, and 70% for NAPI in PRD. • Site-specific management strategies for N and P were needed in the PRD. [ABSTRACT FROM AUTHOR]