This study aims to elucidate the effects of dissolved oxygen (DO) on aerobic granular sludge (AGS) systems treating influent with different organic matter concentrations. Two AGS reactors, i.e. R1 (low organic load) and R2 (high organic load), were operated under DO ranges of 4 mg/L to 6 mg/L and 2 mg/L to 4 mg/L to investigate differences in pollutant removal performance, microbial community structure, and functional gene profiles. The results show that after reducing the DO concentration maintained high removal efficiencies of chemical oxygen demand (COD) and total phosphorus (TP) in both reactors. Meanwhile, the rates of endogenous denitrification coupled with simultaneous nitrification increased by 17.54% and 7.05% in R1 and R2, respectively, with corresponding increases of 9.84% and 6.11% in their contribution to total nitrogen removal. Lower DO levels also induced shifts in microbial community structure, enriching functional microorganisms associated with nitrogen and phosphorus removal. In addition, the abundance of genes related to denitrification and intracellular carbon utilization increased, promoting enhanced nutrient removal performance in the AGS systems. Furthermore, DO variation exerted a more pronounced effect on the low-organic system (R1), indicating that more accurate DO control is required in such conditions for optimal operation.