The relation between floc structure and membrane permeability was studied in a coagulation-microfiltration hybrid process. The floc structure changed with some parameters such as the shape, size and homogeniety of primary particle and concentration of natural organic matter (NOM) in the coagulation process. Floc structure was quantified with fractal dimension (dF). Spherical primary particles formed more porous coagulated flocs compared with layered plate-like primary particles. Additionally, large primary particles (3 μm) also were aggregated loosely. Increase in concentration of NOM made coagulated flocs denser. Membrane permeability was improved with cogulated flocs of lower fractal dimension, which tend to have higher porosity and aggregate relatively loosely. These more porous flocs reduce specific resistance of coagulated flocs. The relation between membrane permeability and fractal dimension of flocs was explored in a submerged MF hybrid system as well as in a batch unstirred cell filtration. In case of flocs with lower fractal dimension, membrane permeability was enhanced.