The challenge of membrane fouling persistently hinders the advancement of membrane technology. The construction of patterned membrane surfaces is anticipated to mitigate the effects of membrane fouling significantly. In this study, ceramic microfiltration membranes with corrugated patterns were fabricated by 3D printing combined with the dip-coating process. To assess the impact of surface patterning on ceramic membrane performance, we initially compared the pore size and pure water flux between straight and corrugated membrane tubes. Both configurations exhibited similar parameters: a support pore size of approximately 1 μm, a membrane layer pore size of about 110 nm, and a pure water permeance of around 950 L m−2 h−1·bar−1. The corrugated ceramic membranes demonstrated superior anti-fouling properties compared to their straight counterparts during the filtration of nanoparticle suspensions, oil-in-water emulsions, and bacterial suspensions. Specifically, under a nanoparticle suspension concentration of 2000 ppm, a transmembrane pressure of 0.2 MPa, and a flow rate of 1.0 m s−1, the corrugated membrane achieved a stable flux of approximately 1.7 times greater than that of the straight membrane. Furthermore, we explored the effects of surface patterning on fluid dynamics through numerical simulations. The enhanced turbulence dissipation rate in the patterned membrane tubes suggests increased surface turbulence and an improved capacity to remove contaminants. This research offers novel insights into the development of ceramic membranes with enhanced anti-fouling capabilities for water treatment.