In order to comprehensively utilize Flos Sophora resources and industrialized large-scale production, the development of optimal conditions for the purification of rutin by polyamide resins is highly desirable. Paraphlomis jauanica was used as the raw material, and four factors including concentration of sample solution, flow rate of the sample solution, ethanol concentration of the eluent and elution volume were investigated to ascertain its influence on the purification of rutin. When the concentration of the sample was 0.286 mg/mL, flow rate of the sample solution was 1.0 mL/min, with eluent of 80% ethanol and elution volume of 2.5 BV. Finally, the yield of rutin was 55.49% and the purity was 99.08%.