The migration and transformation of nitrogen (N) in nature is a key process to maintain the ecosystem balance. In natural water, N-transforming microorganisms in river sediments play a crucial role in the process of N conversion. In order to investigate N distribution in rivers and the sediment microorganism driving processes, this paper studied N distribution in the upper reaches of the Minjiang River, and the composition and function prediction of microbial communities in sediments. Results showed that the sediment ammonium salt was high while the sediment nitrate was lower in the upper reaches of the Minjiang River at high altitude (＞3000 m), and the water nitrite was significantly higher in the 2000-3000 m altitude reaches than that in other altitude reaches. Meanwhile, the distribution of N components was affected by environmental factors such as pH, dissolved oxygen and flow velocity. The sediment bacterial communities were mainly affected by sediment-N components and dissolved organic carbon, while the archaea community was mainly affected by altitude, sediment-N composition and soil organic carbon. The similarity of potential nitrogen-transforming microbial communities showed a significant decline pattern in geographical space, and the potential N-transforming archaea communities in the high altitude reaches were significantly different. Among them, the potential nitrifying archaea were the dominant bacterial group in the upper reaches of the Minjiang River, and the potential nitrifying archaea and potential dissimilating nitrate reducing archaea were significantly higher in the high altitude reaches than in the low altitude reaches. For different processes,Nitrososphaerales, Nitrososphaeraceae and Nitrososphaeraceae are the dominant microorganisms in the nitrification process, andFlavobacteriumis the main group in the N reduction process.Clostridium_sensu_stricto_1andBradyrhizobiumare the main groups in N fixation.Xanthobacter ,Paracoccus and Pseudomonasare the main groups in denitrification. This paper reveals that nitrogen distribution in the upper reaches of the Minjiang River at high altitude is mainly driven by potential sediment-N transforming archaea, these results can provide theoretical support for the ecological management strategy of the upper reaches of the Minjiang River.