Ultrafiltration is an effective method to improve the purity of pectin, but membrane fouling is an urgent problem to overcome. In this work, trisodium citrate, sodium caseinate and calcium caseinate were combined with ultrafiltration to separate and purify pectin extract. The molecular weight cutoff (MWCO) of the ultrafiltration membrane and the sodium citrate concentration were optimized using the color and clarity of the pectin extract as indices, and the influence of sodium citrate on the pectin particle size and zeta potential was further studied. Finally, the pectin extraction yield, some physicochemical indices, including galacturonic acid (Gal A) content, esterification degree, and ash content, and the surface morphology of the pectin particles were measured. The results showed that the ultrafiltration membrane fouling was effectively controlled and that the steady-state flux increased by 2-fold when the pectin extract was treated with a polyether sulfone (PES) UF membrane (100 kDa) in combination with sodium citrate at a concentration of 0.25 mg/ml. The pectin extraction yield increased to 16.4%, and the resulting pectin was a higher-ester refined pectin with a Gal A content of 89.7%, DE content of 77.42%, and ash content of 0.63%. The combination of sodium citrate and ultrafiltration was beneficial not only for improving the permeability and separation performance of the ultrafiltration process but also for providing an example of a monovalent salt as a precipitation agent.