In this study a novel aerobic granular sludge membrane bioreactor (AGMBR) was developed and its performance was compared with that of a traditional membrane bioreactor (MBR). The findings of membrane filtration at the flux of 12 L/m2 h showed that the fouling rate of the AGMBR was 0.490 kPa/day, half that of the MBR. Resistance analysis implied that the cake resistance was the major fouling factor in the MBR, up to 67.2% of total resistance, while pore blocking was the key fouling factor in the AGMBR, accounting for 50.3%. Aerobic granules maintained stability in the AGMBR with a size of 1.2–1.5 mm and a sludge volume index (SVI) of 60–70 mg/L. It was therefore possible to reduce cake resistance and fouling rate. In addition, the concentration of soluble extracellular polymeric substances (sEPS) in the AGMBR was 33.1 mg/L, three times lower than that of the MBR, which resulted in a reduction in membrane fouling for the AGMBR compared with the MBR.