Flow patterns in stirred and aerated bioreactors are greatly influenced by the air flow rate and the stirrer’s rotation speed, which in turns, affects the granulation of aerobic sludge. A three-dimensional computational fluid dynamics (CFD) model was used to simulate the flow pattern under different combination of rotation speeds and superficial gas velocities (SGVs) in a lower ratio of height to diameter (H/D ratio) bioreactor with a plastic cuboid baffle agitator. Simulations showed that flow pattern transited from a single circulation cell to multiple vortical cells with increase of the rotation speed and SGV. Increase in rotation speed had a more significant contribution to gas holdup, liquid velocity, bubble size distribution, flow pattern and shear rate than that of SGV. A stirred and aerated SBR was established to perform aerobic granulation with rotation speed at 300 rpm and SGV at 1.05 cm/s, and the average shear rate of the bioreactor was investigated. The experiment results showed that aerobic granules were successfully formed with filamentous bacteria entangling on the surface of granules. The filamentous granular sludge had good settleability with a settling velocity at 19.6 ± 5.1 m/h, and its SVI value was between 30 and 90 mL/g. The diameter of the granules was up to 1.42 mm. The average shear rate of the bioreactor (12.62–27.52 1/s.) was mostly influenced by the rotation speed rather than the SGV.