In this study, three SBR reactors R1, R2, and R3 were set up and operated using (A/O)-SBR gradient aeration, (A/O)-SBR constant aeration, and the conventional (A/O)-SBR mode, respectively. The nutrient removal performance and aerobic granular sludge characteristics under these aeration modes were explored using real municipal wastewater as the influent matrix. The experimental results revealed that for the R1, R2, and R3 particles during the stable period, the average removal rate of COD was 88.68%, 89.05%, and 88.96%, respectively, the average removal rate of TN was 76.97%, 71.99%, and 64.92%, respectively, the average removal rate of TP was 96.28%, 85.05%, and 78.97%, respectively, and the proportion of denitrifying phosphorus accumulating bacteria to phosphorus accumulating bacteria was 25.52%, 19.60%, and 12.77%, respectively. The results showed that the operation mode of anaerobic, aerobic, and anoxic was more conducive to the enrichment of denitrifying phosphorus accumulating bacteria (DPAOs), and that the gradient aeration was more enriched than the constant aeration mode, which is of great significance to low-intensity municipal domestic sewage treatment with an insufficient carbon source. At the same time, the dissolved oxygen in the aeration section of R1 was reduced step-by-step, which improved the simultaneous nitrification and denitrification rates of particles and the utilization rate of the internal carbon source, which was beneficial for the efficient removal of TN. The particle size of the three groups of reactors was 727.368, 815.072, and 895.041 μm respectively. As the transfer rate of the matrix decreased with particle size, the microorganisms in R2 and R3 may have caused anaerobic respiration to release harmful gas, thus damaging the particle structure, such that the particles in R2 and R3 were less dense than those in R1. In addition, the PN/PS values of R1, R2, and R3 were 6.31, 5.63, and 4.83, respectively, and the EPS content (in terms of VSS) was 103.97, 92.22, and 76.98 mg·g, respectively, at the time of particle stabilization, which revealed that the mode of intermittent gradient aeration was beneficial to stimulate the secretion of EPS. This was especially the case for the secretion of PN, which increased the PN/PS value, enhanced the cell hydrophobicity, and made the particles dense and stable.