Abstract: Microbial communities play a crucial role in the nitrogen cycling process of freshwater river ecosystems. However, little is known about how environmental factors are associated with nitrogen-cycling functional microbial groups in the Yarlung Zangbo River Basin. In this study, the upper reaches of the Linzhi section of the the Yarlung Zangbo River were selected as the study area to investigate the effects of environmental factor variations on nitrogen-cycling-related microbial communities. The results show that variations in microbial community structure were significantly correlated with environmental factors such as TN, TP, and COD_Cr. Mantel's heatmap showed a significant positive correlation between NH₃-N and microbial community abundance, while COD_Cr was significantly negatively correlated with NO₃^--N, and pH was significantly negatively correlated with TP (P < 0.05). Human activities, together with environmental changes, profoundly influenced microbial community succession. Intensive human activities around Milin Airport, a major transportation hub, caused strong disturbances to the riverine aquatic ecosystem. Accordingly, the microbial community structures at sampling point D12 near Milin Airport and at sampling point D6 between Lang County and Milin differed significantly from those at the other sampling sites.Proteobacteria, Actinobacterota, and Bacteroidota were the dominant phyla across all samples. Constrained by environmental factors such as water temperature, TN, and TP, the abundance of nitrogen-cycling functional modules in the study area was generally low. Co-occurrence network analysis show that there were 171 nodes of nitrogen-cycling-related microorganisms, indicating that a wide range of microorganisms responded to nitrogen cycling. Human activities had a significant enhancing effect on the nitrogen-cycling microbial functional groups. This study reveals the distribution characteristics of microbial communities and nitrogen-cycle-related microorganisms in the upper reaches of the Linzhi section of the Yarlung Zangbo River under anthropogenic disturbance, clarified the key environmental driving factors, and can thereby provide a scientific basis for ecological protection and nitrogen-cycling-related research in the Yarlung Zangbo River.