Algae-bacteria interactions play an essential role in the transformation of complex organics in microalgal-bacterial granular sludge (MBGS), but the intrinsic removal mechanisms have not been well understood. This study thus attempted to investigate the removal performance and mechanisms of complex organics in real municipal wastewater in MBGS process. The results showed that complex organics could be effectively disposed during day-night cycles by MBGS, with the process performance significant impacted by the influent C/N ratio. Further metagenomic and metatranscriptomic analyses revealed that the upregulated gap2 and gpmA genes of glycolysis enhanced the conversion of complex organics to CO2 mediated by Chlorophyceae and Acidobacteriae/Sumerlaeia/Fimbriimonadia, while the upregulated petH gene of NADPH synthesis by Cyanobacteria strengthened the fixation of CO2 into biomass. Meanwhile, the functional gene of amyA in the starch metabolism by Actinobacteriota was upregulated, along with the upregulated gldA gene in the glycerolipid metabolism through Chlorophyceae and Chloroflexia/Verrucomicrobiae. Moreover, a close symbiotic relationship between Cyanobacteria and Desulfobacterota I was identified, which played a crucial role in fatty acid decomposition. This study offers new insights into degradation mechanisms of complex organics via microalgal-bacterial symbiosis, which also gains basic knowledge on the carbon cycle in natural water ecosystems mediated by microalgal-bacterial symbiosis.