Metal–organic frameworks (MOFs) are attractive crystalline materials for membranes due to their diverse crystalline pore structures and molecular separation properties. However, the fabrication cost is relatively high compared to conventional polymeric membranes. The concern of the cost could be eased if they are part of a value‐added device, for example, as the key separation unit in a lab‐on‐a‐chip device. This study demonstrates the feasibility of miniaturization of MOF membranes by patterning the membrane surface, a necessary step for MOF membranes to be used in compact devices. Water‐stable ultrathin UiO‐66 membranes with a thickness down to 250 nm on a substrate with a complex pattern were grown. The patterned membranes showed a 100 % improvement in the apparent permeation flux over conventional flat‐UiO‐66 membranes without compromising the molecular separation property, indicating the complexity of a surface would not be a formidable obstacle to the MOF membrane fabrication.