Incurred rabbit plasmas samples were utilized for method quality assessment in this study, where an optimized protein precipitation method for the preparation of rabbit plasma samples and a rapid and sensitive liquid chromatography–electrospray ionization-mass spectrometry for the simultaneous determination of berberine, palmatine and jatrorrhizine was described. Plasma samples (100 μl) were pretreated by protein precipitation with the mixture of 3% formic acid and 50 ng/ml clozapine (internal standard) in acetonitrile followed by LC analysis using a C18 column and a mobile phase composed of 0.4% formic acid solution and 0.2% formic acid solution of methanol (60:40, v/v) operated at a flow rate of 0.4 ml/min. The analysis was performed in the multiple reaction monitoring mode via electrospray ionization source operating in the positive ionization mode. The method was linear over the concentration range of 0.1–400 ng/ml for all target components. The lower limits of quantification were 0.1 ng/ml for all analytes, all intra- and inter-day precision values were less than 7.10%, and accuracy (bias, %) was within ±7.11%. The mean absolute recovery was more than 72% for all analytes. The validated method has been successfully applied to the pharmacokinetic study of berberine, palmatine and jatrorrhizine in rabbit plasma after oral administration of San-Huang decoction to rabbits.