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Algae–bacteria systems are used widely in wastewater treatment. N-hexanoyl-L-homoserine lactone (AHL) plays an important role in algal-bacteria communication. However, little study has been conducted on the ability of AHLs to regulate algal metabolism and the carbon fixation ability, especially in algae–bacteria system. In this study, we used the Microcystis aeruginosa + Staphylococcus ureilyticus strain as a algae–bacteria system. The results showed that 10 ng/L C6-HSL effectively increased the chlorophyll-a (Chl-a) concentration and carbon fixation enzyme activities in the algae–bacteria group and algae group, in which Chl-a, carbonic anhydrase activity, and Rubisco enzyme increased by 40% and 21%, 56.4% and 137.65%, and 66.6% and 10.2%, respectively, in the algae–bacteria group and algae group, respectively. The carbon dioxide concentration mechanism (CCM) model showed that C6-HSL increased the carbon fixation rate of the algae–bacteria group by increasing the CO2 transport rate in the water and the intracellular CO2 concentration. Furthermore, the addition of C6-HSL promoted the synthesis and secretion of the organic matter of algae, which provided biogenic substances for bacteria in the system. This influenced the metabolic pathways and products of bacteria and finally fed back to the algae. This study provided a strategy to enhance the carbon fixation rate of algae–bacteria consortium based on quorum sensing.