In order to understand the sediment bacterial diversity of the upper reaches of the Hanjiang River and its tributaries, as well as the relative importance of deterministic and stochastic processes in the construction of sediment bacterial community, the impact of environmental factors on bacterial community composition was analyzed based on the Illumina high-throughput sequencing technology, the difference of sediment bacterial communities in different seasons was investigated using the non-metric multidimensional scaling (NMDS) method, and the impact of deterministic and stochastic processes on community construction was quantified by combining the neutral community model and the normalized stochasticity ratio. The results show that the bacterial communities in the upper reaches of the Hanjiang River and its tributaries are mainly composed of Proteobacteria, Bacteroidetes, Cyanophyta, Planctomycetes, and Acidobacteria. Bacterial communities differ significantly in different seasons. Geographical distance and environmental factors have little effect on the structure of bacterial communities, and the deterministic process did not play a leading role in bacterial community composition. The stochastic process greatly affected the composition of the community in autumn and spring, and the stochastic process is the dominant factor in the construction of sediment bacterial community.