To develop and characterize novel microalgae-based technology under different mixed light-emitting diode (LED) light wavelengths for simultaneous treatment of actual aquaculture tailwater and biogas upgrading, the performance of four microalgal cultivations in bamboo shrimp aquaculture tailwater treatment and biogas upgrading were systematically examined and analyzed. The results demonstrated that Chlorella vulgaris (C. vulgaris)-endophytic bacterium (S395-2)-Clonostachys rosea (C. rosea) symbiont had the highest growth rate, daily production rate and carbonic anhydrase activity at the 7th d treatment time-point under Red(5): Blue(5) LED mixed light source. After 10d treatment, the nutrient removal efficiency of C. vulgaris-S395-2-C. rosea symbiont under Red(5): Blue(5) LED mixed wavelengths reached up to 93.7% for total inorganic nitrogen, 97.4% for ammonium nitrogen, 96.9% for nitrate nitrogen and 98.8% for phosphate; carbon dioxide (CO2) removal rate maintained at 53.1% without significantly affecting methane (CH4) level. In summary, the present study demonstrates that Red (5): Blue(5) LED mixed wavelengths optimally increase the performance of C. vulgaris-S395-2-C. rosea symbiont in nutrient and CO2 removal without loss of CH4, providing a framework for future simultaneous performing actual aquaculture tailwater treatment and biogas upgrading using microalgae-endophytic bacteria-fungus symbiont.