In this paper, three identical membrane bioreactors (MBRs) were operated in parallel in order to specify the influence mechanism of hydraulic retention time (HRT) on MBR. The results showed that the removal efficiency of chemical oxygen demand (COD) was stable though it decreased slightly as HRT decreased, but biomass activity and dissolved oxygen (DO) concentration in sludge suspension decreased as HRT decreased. The filamentous bacteria grew easily with decreasing HRT. The extracellular polymeric substances (EPS) concentration and sludge viscosity increased significantly as filamentous bacteria excessively grew. The over growth of filamentous bacteria, the increase of EPS and the decrease of shear stress led to the formation of large and irregular flocs. Furthermore, the mixed liquid suspended solids (MLSS) concentration and sludge viscosity increased significantly as HRT decreased. The results also indicated that sludge viscosity was the predominant factor that affecting hydrodynamic conditions of MBR systems.