A complex-function fluid controller placed in front of a membrane module was used to control the velocity change with feed fluid and reduce membrane fouling. Using humic acid as the simulated pollutant, the effects of the square wave function, sine function, reciprocal function, and power function feeding on the membrane flux were investigated. For sine function feeding, the membrane-specific flux was the largest and was maintained above 0.85 under the intermittent frequency of 9 s. Compared with the final membrane-specific flux with steady-flow feeding of 0.55, functional feeding could significantly reduce membrane fouling. SEM results showed that sine feeding led to slight contamination on the membrane surface. Furthermore, the Computational Fluid Dynamics (CFD) simulation results showed that the shear force of sine function feeding was about three times that of the steady flow (6 × 105 N). Compared with steady feeding, functional feeding could significantly improve the shear force on the membrane surface and reduce membrane fouling.