The object of this study is to clarify the effect of membrane surface morphology on membrane fouling with sodium alginate (SA) which is a kind of natural organic matter (NOM) and is considered to be the main foulant in membrane water treatment. Cellulose acetate butyrate polymer which is superior in heat-resistance and mechanical strength was used as membrane material. Four kinds of membranes having different surface and cross-sectional structures were prepared via thermally induced phase separation and non-solvent induced phase separation. In the case of the filtration of 50 mg L −1 SA solution from the outer surface to inner surface, the membrane having the dense outer surface showed higher permeability and higher recovery of permeability by backwashing. An addition of calcium chloride into the sodium alginate solution resulted in significant flux decline due to thick cake layer formed by cross-linking of sodium alginate. In this case, the membranes with the dense outer surface also showed higher permeability. Furthermore, it was found that membrane fouling with sodium alginate took place mainly on the outer surface rather than inside the membrane by measuring infrared absorption spectrum of the membrane after filtration of sodium alginate solution with and without calcium chloride.