New methods based on MEEKC coupling with field-amplified sample injection (FASI) induced by ACN were proposed for five isoquinoline alkaloids (berberine, palmatine, jatrorrhizine, sinomenine and homoharringtonine) in no salt and high salt sample solution (HS). For the separation of five isoquinoline alkaloids, a running buffer composed of 18 mM sodium cholate, 2.4% v/v butan-1-ol, 0.6% v/v ethyl acetate, 10% v/v (or 30% v/v) methanol and 87.0% v/v (or 67% v/v) 5 mM Na2B4O7~10 mM NaH2PO4 buffer (pH 7.5) was developed. In order to improve the sensitivity, FASI induced by ACN was applied to increase the detection sensitivity. The detection limit was found to be as low as 0.0002 microg/mL in no salt sample solution and 0.062 microg/mL in HS. The method has been applied for the analysis of human urine spiked with analytes, and the assay results were proved to be satisfactory, and also the determination of berberine in urine sample after oral administration berberine.