Abstract Previous studies have demonstrated the improved membrane properties of ceramic membranes made from thermally modified clays with cationic manioc starch and eggshell residue as additives. Based on the employment of these membranes, the relationship between thermally modified clays’ structure and cross-flow microfiltration using oil-in-water emulsion was studied (North Sea heavy crude oil). Using raw clay (M1) and thermally pretreated clay (M2), tubular ceramic membranes were prepared by the extrusion method. Critical Flux in different concentrations (250, 500, and 1000 mgL−1), fouling mechanisms, and membrane resistance were analyzed. The initial membrane resistance values for M1 and M2 membranes were 2.23 ± 0.32 × 1012 m−1 and 1.72 ± 0.293 × 1012 m−1, respectively. The membrane resistance was reduced by 22% due to the clay modification, which also decreased the contact angle, increased the pore size, and decreased the membrane roughness. Regarding the total organic carbon removal, the M2 membrane had no loss in separation efficiency despite having a slightly larger pore size. These results indicate that the clay-induced structural changes decreased the membrane resistance and improved the permeate flux but did not decrease the oil-in-water emulsion’s separation efficiency.