In order to elucidate the mechanism of the influence of dissolved oxygen (DO) on the aerobic granular sludge (AGS) system, the differences in pollutant removal, microbial community structure and functional genes of AGS systems with different influent organic matter concentrations were studied under the conditions of 4-6 mg/L and 2-4 mg/L, respectively. The results showed that after the DO concentration was reduced, the COD and TP removal rates of low-organic reactor R1 and high-organic reactor R2 remained high, while the endogenous denitrification rates of synchronous nitrification increased by 17.54% and 7.05%, respectively, and the contribution rate of endogenous denitrification to nitrogen removal increased by 9.84% and 6.11%. The decrease of DO drove the adjustment of microbial community structure, promoted the increase of the abundance of functional bacteria for nitrogen and phosphorus removal in AGS, and improved the abundance of denitrification and genes related to internalized carbon sources, which was conducive to achieving good phosphorus and nitrogen removal performance in AGS system. The study also found that DO changes have a more significant impact on low-organic AGS systems, and more accurate DO regulation should be implemented in actual operation. This study provides a theoretical basis for long-term stable nitrogen and phosphorus removal in AGS system.