This study reported the role and significance of extracellular polymeric substances (EPSs) on nutrients storage and transfer in an algal-bacteria symbiosis sludge (ABSS) system for wastewater treatment, and the novel algae-based sequencing batch suspended biofilm reactor (A-SBSBR, Ra) was selected as model of ABSS system. Results showed that compared to conventional SBSBR, the EPS of Ra performed better storage for NO2–-N, NO3–-N, total phosphorus and PO43− -P, with increase ratios of 43.7%, 36.0%, 34.1% and 14.7% in sludge phase and 174.0%, 147.4%, 150.4% and 122.0% in biofilm phase, respectively. The analysis of mechanisms demonstrated that microalgae active transport and uptake for divalent cations could enhance their local concentrations around ABS flocs and partially neutralized negative charge of EPSs, and more anions related to nutrients were absorbed in EPSs. Moreover, O2 produced by microalgae photosynthesis enhanced bacteria activity and improved the production of EPSs in both sludge and biofilm phases.