External aeration significantly influences microalgae consortium performance in municipal wastewater treatment. This study evaluated two Chlorella strains and mixed cultures under daytime, nighttime, and continuous aeration modes at 50 and 200 mL/min. Distinct aeration preferences were observed among microalgal strains, necessitating tailored strategies for mixed microalgae. Aeration mode had a greater impact on microalgae consortium performance than aeration intensity. Intermittent aeration enriches functionally differentiated microorganisms and reduces random contributions to microbial assembly. High intermittent aeration (DA_200 and NA_200) achieved the highest pigment accumulation in Chlorella pyrenoidosa (20.49 mg/L), while the mixed culture under CA_200 averaged only 5.36 mg/L. Nighttime mode promoted pigment accumulation in microalgae and enriched heterotrophic bacteria, enhancing organic pollutant degradation. Daytime mode favored the enrichment of simultaneous nitrification-denitrification bacteria, improving nitrogen removal efficiency. Meanwhile, continuous mode reduced microalgal growth by promoting complete nitrification and reducing nitrogen availability. Optimizing aeration strategies enhances microalgae consortium performance and wastewater treatment solutions.