Bosten Lake is a typical inland lake in the arid and semiarid region of northwestern China. However, the influence of the dissolved organic matter (DOM) source composition on the bacterial community structure and diversity across various functional zones, as well as the role of the bacterial community structure in regulating DOM composition, remains unclear. In this study, we combined excitation-emission matrix (EEM) fluorescence spectroscopy with the parallel factor analysis (PARAFAC) method to investigate the characteristics and source distribution of the DOM fluorescence components in the water of Bosten Lake. The bacterial community characteristics in both water and sediment samples were analysed through high-throughput sequencing. The relationships among bacterial communities, DOM fluorescence components, and environmental factors were elucidated through principal component analysis and redundancy analysis. The results revealed that (1) the DOM of Bosten Lake contained three humus-like fractions and one protein-like fraction, with endogenous proteins being the primary source of DOM, complemented by exogenous humus inputs. (2) The richness and diversity of bacterial communities in sediments are significantly higher than those in water bodies, among which Proteobacteria dominate the composition of bacterial communities. (3) Ammonia nitrogen (NH4+-N) significantly influenced the bacterial community composition, with microorganisms associated with the nitrogen cycle dominating the bacterial community in both water and sediment. Total dissolved solids (TDS) is a key factor influencing the composition of bacterial communities in water bodies. Across all sampling sites in Bosten Lake, the mean TDS concentration was 900 mg/L, with high levels causing structural damage to microbial enzymes (4) The DOM fluorescence component explained 64.9% of the variation in the bacterial community composition, indicating a strong response relationship between bacterial communities and DOM components. Overall, these results provide a scientific basis for the protection of the ecological environment of Bosten Lake.