Aerobic denitrification has become a research hotspot in biological denitrification in recent years due to its unique advantages. Dissolved organic matter (DOM) as a carbon source is the important reason for community differences. To explore the responding mechanism of aerobic denitrifying bacteria community structure to dissolved organic matter in different functional areas of Lake Baiyangdian, this paper combines the fluorescence area integration method and the high-throughput sequencing technology of napA denitrification genes to study the characteristics of the aerobic denitrifying bacterial community structure and responding mechanism in Lake Baiyangdian. The results showed that the concentration of protein-like components was higher than that of humic-like components in the organic matter of Lake Baiyangdian sediments in spring. Among them, the protein-like components in the culture area were the largest, reaching 79.63%±3.79%, and the humus-like component in the primitive area was the largest, reaching 33.91%±6.32%; A total of 3693 OTUs were acquired high Throughput sequencing, which was divided into 9 main phyla. Among them, the Proteobacteria accounted for the largest proportion, reaching over 99%; the α diversity Chao1 index showed significant spatial differences, and the travel area>the living area>the entry area>the original area>the breeding area; the main species of aerobic denitrifying bacteria include Aeromonas, Sulfuritortus, Cupriavidus, Pseudomonas and Thaurea, Ferrimonas, as an indicator species, contributes the most to the difference; Redundant analysis found that the components of fulvic acid-like substances and microbial metabolites in the visible light area are the main reasons for the differences in aerobic denitrifying bacteria in different functional areas. In summary, this research will not only help to further understand the characteristics of the nitrogen cycle microorganisms in the natural environment; it will also provide a reference for the selection of carbon sources suitable for efficient bacterial screening in the practical environment.