This study focused on the contamination mechanism and regeneration strategies of sulfopropyl ion exchange resin (SP Sepharose FF) during the separation of recombinant human lactoferrin from transgenic bovine milk. We analyzed primary constituents’ contents in chromatorgraphic material and fractions. The results showed that the lipid in milk can clog the column or adhere to the resin through hydrophobic interaction, leading to an increase in column pressure. Some casein molecules were found to adsorb onto the resin through electrostatic interaction, therefore the adsorption capacity was decreased. There was no direct interaction between lactose and the resin in the chromatorgraphic process. Increased continuous chromatographic cycles and prolonged time interval between protein purification and column regeneration could enhance the undesirable interaction between the contaminants and resin, thus lowering the regeneration efficiency. NaOH was found to be effective in the removal of lipid and casein molecules from the column. Furthermore, normal microstructure and chromatographic performance of the ion exchanger was recovered after this cleaning procedure.