Zoobenthos is an indispensable constituent of lake eco-environment and plays an important role in nitrogen cycle between sediment and water. Zoobenthos is the potential source of N₂O emission. However, it is still need to further study on the N₂O emission mechanism of zoobenthos in the region of algal accumulation. Thus, the combining gas chromatography with modern molecular biological techniques was used to analyze the N₂O emission flux and intestinal microorganism to extend our knowledge about the microbiological mechanism of N₂O emission in eutrophic lake. The results showed that the N₂O emission flux of the gut of Chironomus plumosus larvae decreased about 60%, which accounted for 77% of the total emission flux form C. plumosus, indicating that the gut was the major N₂O emission site of C. plumosus larvae. The intestinal bacterial diversity of C. plumosus larvae would decrease with the presence of algal bloom, while the bacterial community structure also changed, the relative abundance of β-proteobacteria increased 21%, whereas δ-proteobacteria decreased 62%. The diversity of nirS-type denitrifiers was higher and their sequences were related to different phylotypes to converse more nitrate to nitrite. Hence, algal bloom increased the richness and diversity of intestinal denitrifying bacteria. The data obtained in this study further elucidates that the algal bloom decreased the emissions of N₂O from the zoobenthos in freshwater sediment and could be useful to better understand the environmental effects of zoobenthos and the nitrogen cycle in freshwater ecological systems.