A new and low-cost method to isolate and purify glucoraphenin as a potassium salt from radish seeds was described in this article. Crude glucoraphenin was separated from radish seeds, and then used as raw material for further purification of glucoraphenin by low-pressure column chromatography. Compared with K2SO4 solution, KCl solution is a preferable eluent for increasing the purity and recovery of glucoraphenin, and reducing the usage of salt. In order to remove a large quantity of KCl, nanofiltration with NF270-400 membrane and precipitation with methanol were investigated. Consequently, compared with precipitation, the purity and recovery of glucoraphenin prepared by nanofiltration were both much higher. At the same time, nanofiltration also got better efficiency of desalination. The purity of glucoraphenin was 91.5%, the recovery of it was 89.0%, and the removal of KCl was 99.5%. The glucoraphenin product was identified by MS, 1H, and 13C NMR spectra.