In a coagulation−microfiltration (MF) hybrid process, membrane permeability and permeate water quality were investigated in conjunction with coagulation mechanisms under two kinds of dead-end (e.g., submerged and external pressure type) and cross-flow microfiltration modes. The specific cake resistance of coagulated suspension largely depended on coagulation condition, being lower at charge-neutralization than that at sweep-floc condition. The lower specific cake resistance was attributed to the formation of less compressible but more porous cake with the charge-neutralization condition. Under the dead-end MF modes, the effect of coagulation condition was clearly demonstrated on the rising rate of transmembrane pressure at constant flux, e.g., membrane permeability with charge neutralization turned out to be much better than that with sweep-floc mechanism. The trends of specific cake resistance are in good agreement with the difference in membrane permeabilities between the two dead-end filtration modes. Under the cross-flow microfiltration mode, however, the coagulated suspensions formed via the two different mechanisms showed almost the same steady-state flux. It was because the portion of particles that otherwise deposit or adsorb on the membrane was reduced, and thus the effect of different specific cake resistance was mitigated. It was confirmed by the analysis of back-transport velocities, feed, and permeate water quality and also by the measurement of particle size distributions involved in the coagulation−cross-flow microfiltration. The permeate water quality was also examined in terms of the removal of natural organic matter (UV254, TOC) and residual aluminum concentration.