Due to human activities, the overabundance of regional nitrogen/ phosphorus (N/P) has a huge impact on ecological environment worldwide. It’s quite necessary to comprehensively understand the human-induced N/P inputs and spatiotemporal variations of nutrients in the river. As the adjustment to the spatial structure of Beijing, the Beijing’s sub-center is an important strategic position in promoting the coordinated development of Beijing-Tianjin-Hebei. In this study, the dynamic changes of NH ₃N and TP from 2012 to 2022 were analyzed, then the net anthropogenic N input (NANI), net anthropogenic P input (NAPI) was estimated in the Beijing’s sub-center. The results showed that both NH ₃N and TP had an overall downward trend with a three-stage pattern. The NANI and NAPI declined from 5.68 x 10 ⁴ kg∙km ⁻²∙a ⁻¹ and 0.95 x 10 ⁴ kg∙km ⁻²∙a ⁻¹ to 0.78 x 10 ⁴ kg∙km ⁻²∙a ⁻¹ and 0.15 x 10 ⁴ kg∙km ⁻²∙a ⁻¹, respectively. The chemical fertilizers input accounted for the largest part at 53%~81% of NANI and 49%~80% of NAPI. There were high values of N and P input in the southeast of Tongzhou, and the fluxes of N and P were positively correlated with the inputs of anthropogenic N and P in the Chaobai River Basin and the Beiyun River Basin. This study would provide the foundation for setting priorities and enacting more targeted N/P management strategies in the Beijing’s sub-center.