• Engineering of ceramic membranes (CMs) leads to better filtration performance. • Microstructures are integrated with surface chemistry and functionalities in CMs. • Surface-patterned and gradient CMs are realized by additive manufacturing techniques. • Functionalized CMs promise for antifouling and high-efficiency filtration. Ceramic membranes are being increasingly applied in water/wastewater treatment, chemical, beverage and pharmaceutical industry, due to their excellent filtration/separation performance, chemical, mechanical, thermal and long-term stability. This work presents a comprehensive review on the structure design, chemistry manipulation and functionalization of advanced ceramic membranes for their better performance in water/wastewater treatment. It begins with looking into engineering the microstructure features of advanced ceramic membranes, especially the intermediate and top active layers, aiming at reducing the mass transport resistance and the likelihood of membrane fouling. Strategies to tune both the porosity and pore configuration in the intermediate layer, minimize their thickness and even complete elimination are then analyzed. Recent advances in surface patterning of ceramic membranes enabled by additive manufacturing techniques are also highlighted. In parallel, emerging methodologies in manipulating the chemistry aspects of the top layer, in terms of surface hydrophilicity and surface charges, are examined, in order to regulate the interactions between the membrane surface and water/foulant molecules. Going beyond the conventional membranes, these functionalized ceramic membranes with the coupling of external stimulus are further involved for high-efficiency filtration and antifouling ability, with the focus on structural optimization at various scales. Finally, perspectives and opportunities on the marriage between microstructure and chemistry are discussed for new generation ceramic membranes and their application in water and wastewater treatment.