An ionic liquid modified magnetic nanosilica chain was prepared and used to separation berberine from Coptidis Rhizoma. To increase the efficiency, the adsorption amounts of a serial ionic liquid modified magnetic nanosilica was investigated with berberine standard solution. At 25oC and pH=3.0, the Fe3O4@IL@Sil-C obtained the highest adsorption amount in 3.0 h. Then the sorbent was applied in extraction solution of Coptidis Rhizoma and 0.03 mg/mL of berberine can be separated. The recoveries and RSD were in the range of 92.6-99.8% and 4.6-7.8% highlighting the accuracy of this sorbent.