Aeration, an effective approach to the alleviation of membrane fouling, has been broadly used in the wastewater treatment. Despite the wide application of aeration in the fouling control, the enhancement of surface shear by producing slug bubbling flow within the narrow gap has not been fully understood. In the present research, extensive numerical investigations were carried out to elucidate the dynamics of bubbly flow in the flat-sheet membrane bioreactor with the validation of our experimental results. Conforming to the experiments, the simulations indicated that there exists a transition in the terminal velocity of 1 − 2 mm bubble where the transit of flow pattern was discovered. The transition of bubble shape and its trajectory alters the velocity distribution in the confined zone between the membranes, leading to the change of shear stress and mass transfer properties adjacent to the membranes. Theoretically, the mechanics of how the bubbles within the channel between flat-sheet membranes adjust the velocity gradient near the membrane surface were revealed. Moreover, with the increase of bubble diameter, it was found that the enhancement of shear stress becomes less significant at the cost of greater gas inflow. An optimal range of bubble diameter was proposed to retain a relatively high efficiency of wastewater treatment at the economically-friendly expense of aeration. The outcome obtained from this study provides good guidance for the optimization of bubbling technology and contributes to the development of wastewater treatment.