Due to the diversity and complexity of the components in traditional Chinese medicine (TCM) extracts, serious membrane fouling has become an obstacle that limits the application of membrane technology in TCM. Pectin, a heteropolysaccharide widely existing in plant cells, is the main membrane-fouling substance in TCM extracts. In this study, a hydrophilic hybrid coating was constructed on the surface of a polyvinylidene fluoride (PVDF) ultrafiltration (UF) membrane co-deposited with polydopamine (pDA) and (3-Aminopropy) triethoxysilane (KH550) for pectin antifouling. Characterization analysis showed that hydrophilic coating containing hydrophilic groups (-NH, Si-OH, Si-O-Si) formed on the surface of the modified membrane. Membrane filtration experiments showed that, compared with a matched group (FRR: 28.66%, Rr: 26.87%), both the flux recovery rate (FRR) and reversible pollution rate (Rr) of the pDA and KH550 coated membrane (FRR: 48.07%, Rr: 44.46%) increased, indicating that pectin absorbed on the surface of membranes was more easily removed. Based on the extended Derjaguin-Laudau-Verwey-Overbeek (XDLVO) theory, the fouling mechanism of a PVDF UF membrane caused by pectin was analyzed. It was found that, compared with the pristine membrane (144.21 kT), there was a stronger repulsive energy barrier (3572.58 kT) to confront the mutual adsorption between the coated membrane and pectin molecule. The total interface between the modified membrane and the pectin molecule was significantly greater than the pristine membrane. Therefore, as the repulsion between them was enhanced, pectin molecules were not easily adsorbed on the surface of the coated membrane.