In order to investigate the effects of the three kinds of membrane module’s structures on the NF separation, such as permeate flux and observed rejection, three self-designed flat-plate NF membrane modules and a kind of commercial nanofiltration membrane were used to carry out the experiments. It is shown, from the experimental results of three kinds of membrane module systems (the spiral flow type, the serpentine flow type and the normal flow type), that at the same operating condition, permeate flux is strongly affected by the concentration polarization on the membrane surface, and the flux of the spiral flow module is the largest due to the disturbance of the secondary flows to the concentration polarization, then is that of the serpentine flow module, and follows by that of the normal flow module. When the flow is laminar, the permeate flux of the spiral flow module is about 2 times greater than that of the serpentine flow module. When the flow is turbulent, the permeate flux of the former is about 1.6 times larger than that of the latter. It is also shown that the structures of the membrane module and the permeate flux have great influence on the solute rejection. When the flow is laminar, the Mg2+ rejection of the normal flow module is the greatest, say, up to 94.2%, and that of the spiral flow module is larger than that of the serpentine flow module. When the flow is turbulent, the Mg2+ rejection of the latter is greater than that of the former, e.g. up to 97.1%, for the effect of the secondary flow on the concentration polarization becomes relatively weaker.