<p>In natural aquatic ecosystems, algal-derived organic carbon (AOC) often coexists with exogenous organic carbon (EOC). Microbial utilization of these distinct carbon sources affects carbon flux and transformation in water column and algal growth. <i>Microcystis</i> blooms significantly increase AOC levels in water, but the microbial transformation process of <i>Microcystis</i>-derived AOC in the presence of EOC remain poorly understood. We conducted a simulated experiment by introducing ¹³C-sodium bicarbonate and ¹³C-glucose as substrates for indoor simulation of non-axenic <i>Microcystis aeruginosa</i> (<i>M. aeruginosa</i>) populations in a sealed system. The microbial transformation processes of AOC and EOC and their effects on <i>M. aeruginosa</i> growth were investigated. Results demonstrated that the addition of glucose accelerated <i>M. aeruginosa</i> growth and significantly increased their biomass. During the experiment, as the particulate organic carbon and nitrogen content increased, the concentrations of CO₂ and N₂O were gradually decreased, while the concentration of CH₄ were gradually increased. Significant differences were observed in the microbial processes involved in the uptake of AOC and EOC. Bacteria involved in AOC transformation throughout the growth period were dominated by Proteobacteria, Gemmatimonadota, Actinobacteriota, Bacteroidota, Acidobacteriota, and Firmicutes. The bacteria involved in EOC transformation were dominated by Proteobacteria, Actinobacteriota, Firmicutes, Cyanobacteria, Armatimonadota, and Bacteroidota. Linear discriminant analysis Effect Size (LEfSe) analysis revealed <i>Massilia</i> and <i>Akkermansia</i> as biomarkers involved in AOC transformation, while <i>Ligilactobacillus</i> was associated with EOC transformation. These findings provide valuable insights into the effects of EOC on algae-bacteria interaction, and on the dynamics of carbon and nitrogen cycling among <i>M. aeruginosa</i> and its associated bacteria.</p>