The goal of the present paper is to investigate the aeration process and the enhanced effect of baffles in a full-scale commercial membrane bioreactor (MBR) system configured with a flat sheet (FS) membrane module. Through a computational fluid dynamics (CFD) simulation, two aerated FS membrane modules for full-scale applications with 26 membrane sheets were simulated. The numerical results indicate that the presence of baffles and the distances between the baffle and the outmost membrane sheet have a minor influence on the area-weighted shear stress for full-scale MBRs. In addition, bubble size and the bottom distance between the aerator and membrane bottom do not affect the average shear stress of full-scale FS membrane modules much. However, an increase in air flow rate has a significant effect on the area-weighted shear stress. A large FS membrane module is recommended, as it could achieve the same cleaning effect as the small one with a lower specific aeration demand for membranes.