It has been identified that temperature polarization and concentration polarization are typical near-surface phenomena limiting the performance of membrane distillation. The module design should allow for effective flow, reducing the polarization effects near the membrane surfaces and avoiding high hydrostatic pressure drops across and along the membrane surfaces. A potential route to enhancing the membrane distillation performance is geometry modification on the flow channel by employing baffles as vortex generators, reducing the polarization effects. In this work, various baffles with different structures were fabricated by 3D printing and attached to the feed flow channel shell in an air gap membrane distillation module. The hydrodynamic characteristics of the modified flow channels were systematically investigated via computational fluid dynamics simulations with various conditions. The membrane distillation tests show that adding the baffles to the feed channel can effectively increase the transmembrane flux. The transmembrane flux with rectangular baffles and shield-shaped baffles increases by 21.8% and 28.1% at the feed temperature of 70 °C. Moreover, the shield-shaped baffles in the flow channel not only enhance the transmembrane flux but also maintain a low-pressure drop, making it even more significant.