The aerobic granular sludge (AGS) effectively mitigates the membrane fouling of a membrane bioreactor. However, the role and effects of the concentration polarization (CP), induced during the AGS filtration process on the membrane fouling and membrane cleaning efficiency, remain unclear. In the present study, the AGS resulted in a higher CP proportion (>50%) and a lower CP resistance (<3 × 10 m), compared with the flocculent sludge, owing to the synergistic effect of the hydraulic shear and AGS scouring development, which improved the AGS in suspension and also minimized its deposition on the membrane. High-frequency interactions (contact and collision) between the AGS and membrane enhanced the CP resistance by returning more granular sludge from the cake layer to the CP, which proportionally increased the fouling resistance. Based on the correlation of CP and fouling resistance, the CP resistance was divided into 3 categories: high-intensity (2.76 × 10 m), medium-intensity (1.74 × 10 m), and low-intensity (0.62 × 10 m). At the high-intensity CP, most membrane pores were “sealed” (complete pore blocking [R > 0.9015]) and the pore blocking condition was the most serious (K-value = 0.0622 s), while the membrane surface became denser and rougher. As a result, the permeability loss after the long-term filtration increased. In the chemical cleaning investigation, the alkaline detergents yielded an enhanced membrane cleaning efficiency to recover permeability. By reducing the CP, the membrane cleaning efficiency was marginally improved. The present study reveals the quantitative role of CP and offers insights into the mechanisms that govern membrane fouling in a membrane bioreactor.