Membrane technology is an energy-efficient separation process that is expected to dominate the water treatment industry. However, the high vulnerability of membranes to fouling has limited the expansion of sustainable and energy-efficient membrane processes. Surface patterning has been proven to be an effective method to improve the performance of membranes by increasing the permeate flux and lowering the attachment of fouling materials on membrane surfaces. In this study, a new generation of patterned membranes was prepared using a novel hydrogel facilitated phase separation (HFPS) method. Hydrogel contains a high water content which initiates phase separation as a nonsolvent upon contact with the polymer solution. Structuring a hydrogel mold provides the ability to control the location of the skin layer on the patterned side of the membrane. The performance of the patterned and the unpatterned membranes made with HFPS was examined in a cross-flow filtration system; a significant increase in the pure water flux (~100%) was observed for the patterned membrane. Moreover, a fouling experiment with bovine serum albumin (BSA) solution showed that the patterned membranes maintained 76% higher flux after 90 minutes of operation.