In algae-bacteria symbiotic systems, algae and bacteria work cooperatively to reduce aeration demand and carbon emissions during wastewater treatment. However, controlling and stabilizing microbial communities in the conventional algae-bacteria symbiotic systems are complicated and unstable. We, therefore, developed a novel sewage treatment system based on a filamentous algae-bacterial symbiotic granule system (AB) in a photo-sequencing batch reactor (PSBR). The exogenous signal molecules (i.e., N-acyl-homoserine lactones [AHLs]) were applied to promote the algae-bacteria consortia formation. The characteristics and performance of the mature algae-bacterial granular consortia were investigated and then compared with that of the activated sludge (AS) system under identical operating conditions. The chemical oxidation demand (COD) removal efficiencies were greater than 90% in the dynamic synergistic investigation, even without aeration. However, the addition of AHLs (5, 50, and 200 nmol/L) had a negligible effect on treatment performance. In static conditions, 10 nmol/L of AHLs can significantly regulate the algae-bacteria symbiotic system, and AHLs (<50 nmol/L) improved COD and NH removal efficiencies by up to 90%. Moreover, the addition of AHLs augmented polysaccharide secretion but had little effect on protein secretion. In comparison to the AS system, the AB system demonstrated promise in terms of pollution removal efficiency and microbial diversity enhancement. Practitioner Points: Oscillatoria can serve as an excellent biological carrier for immobilizing bacteria. AHLs (10 mol/L) regulated the operation state of algae-bacteria symbiotic system. AHLs altered the composition and content of EPS in the algae-bacteria system.