As an emerging sustainable process, knowledge of microalgal-bacterial granular sludge (MBGS) for the treatment of complex organic wastewater is limited, which hinders its further technical application. In this work, the MBGS process for the disposal of wastewater with simple and complex organic substances was evaluated in a comparable manner. The results showed that the average COD, nitrogen and phosphorus removal efficiencies for wastewater containing simple/complex organic matter were 75.2/84.9%, 96.6/89.3% and 76.2/85.3%, respectively. It has been found that complex organics can promote granule size growth and bacteria growth, as evidenced by the decrease in chlorophyll content and cellular carbon-nitrogen ratio compared to simple organics. Chloroflexi became the dominant bacterium of MBGS for potential contribution to the breakdown of complex organic matter. In addition, the settling property of MBGS has been improved and the extracellular protein of MBGS has been strengthened by complex organic substances. During a one-cycle reaction, CO2 levels could be reduced by about 300 ppm, suggesting that a carbon-neutral target for wastewater treatment by MBGS is possible. This research complements knowledge of MBGS for real wastewater treatment.