Abstract: NaPF₆ (as an ion-pairing agent) was added to the extraction solution of Rhizoma coptidis and Cortex phellodend containing[C₆MIM] [Br] (as hydrophilic ionic liquid (IL)). A cloudy solution formed as a result of the formation of fine droplets of[C₆MIM] [PF₆]. After centrifugation,the sedimented phase enriched with alkaloids was analyzed by HPLC with UV detection. In this method, several important parameters,such as the type and volume of ILs,the amount of NaPF₆,solution pH,extraction time and centrifugation time,influencing the extraction efficiency of IL-ISFME (in situ solvent formation microextraction) were optimized. Under optimal conditions,berberine,palmatine and coptisine exhibit good linearity,with correlation coefficients of 0.9998,0.9996 and 0.9997,respectively,a linear range of 1~2000 μg/L and the detection limit of 0.5 μg/L. The spiked recovery for each analyte is in the range of 96.52%~104.34%. The experimental results indicate that the proposed method is successfully applied to the analysis of three alkaloids in Rhizoma coptidis and Cortex phellodend.