The effects of different inlet/outlet features and helical structures on the flow pattern and transfer performance of membrane modules were investigated with both three-dimensional computational fluid dynamics and experimental methods. In a circular flat membrane module, two types of inlet/outlet with single-port or three-port configuration were used to evaluate the influence of small differences in the opening area structure of the inlet/outlet on the flow patterns. Although the transfer regions differ, large flow swirls appear in both systems, leading to stagnation regions and causing significant back-mixing. To alleviate the swirls and improve the flow pattern, a helix clapboard was used to separate the membrane feed channel as spiral channel. Both the numerical and experimental results indicate that the helical structure can greatly enhance the transfer performance and increase the permeation rate while the increment in energy consumption is very small.