NaA zeolite membranes have exhibited excellent performance in pervaporation dehydration of organic solvents. However, the industrial applications based on tubular NaA zeolite membranes are limited due to the high fabrication cost and low permeation flux. Hollow fiber supported zeolite membranes have great advantages of high permeation flux and large packing density, which are beneficial to further reduce the membrane cost. For practical application, it is of great significance to design membrane modules with optimized geometric configuration for the hollow fibers. Here, a hollow fiber membrane module equipped with seven bundles of hollow fiber NaA zeolite membranes and several baffles was designed by computational fluid dynamics (CFD) technique. The effect of baffles on flow field distribution of the membrane module was investigated. The results showed that the membrane module with two radial baffles and four axial baffles not only showed uniform flow distributions inside the module, but also improved the axial velocities along the hollow fibers, which could alleviate concentration polarization. The improved separation efficiency of the membrane module was further confirmed by the experimental characterization.