The effect of influent chemical oxygen demand to nitrogen (COD/N) ratio on the granular stability, nutrients removal and accumulation of the algal-bacterial AGS was investigated. Two sequencing batch reactors were operated under different influent COD/N ratio, i.e., R-1 (control, COD/N = 8) and R-2: (COD/N = 8, 4, 2, and 1 through stepwise decrease of COD). Results showed that the integrity coefficient of the granules in R-2 stabilized at 0.7-5.4% during the whole operation. Significantly enhanced dissolved inorganic carbon (DIC) uptake and the faster growth of algae indicated the great potential for reduction in greenhouse gases (GHGs) emission by using the algal-bacterial AGS system. The algal-bacterial AGS biomass contained high phosphorus (P) and N contents as well as extremely high P bioavailability (up to 98%) which could be easily used for resource recovery. Loosely bound extracellular polymeric substances (LB-EPS) might be the key factor to control the deterioration of granular stability in this system.