The isoflavones widely exist in the daily diets and interferences are usually inevitable in the determination of the in vivo level of the same analytes. A new strategy to eliminate the dietary interference was established to evaluate the exposure of isoflavones including daidzin, glycitin, genistin, daidzein, glycitein, and genistein in rats fed with Semen Sojae Praeparatum (SSP) extract. Plasma samples were pretreated by liquid-liquid extraction with ethyl acetate using quercetin as the internal standard (IS). The chromatographic separation was achieved on a Symmetry C18 column (100 mm × 3.0 mm) using a gradient mobile phase consisting of acetonitril and water (containing 0.1% formic acid) with a run time of 13.0 min at a flow rate of 0.4ml/min. The detection was carried out by a triple–quadrupole tandem mass spectrometer in multiple reaction monitoring (MRM) mode via polarity switching between negative (for and positive (for daidzin glycitin) ionization mode. All calibration curves exhibited good linearity (r> 0.99) over a wide concentration range for all components. The lower limit of quantitation (LLOQ) was in the range of 0.1–0.4 ng/ml. The intra-day and inter-day precisions (RSD) at three different levels were both less than 14.9% and the accuracies (RE) ranged from −9.3% to 14.5%. The extraction recoveries of the analytes and the IS ranged from 85.7% to 100.2%. The validated method was first successfully applied to pharmacokinetic study of the six isoflavones in rat plasma after oral administration of SSP extract. The dynamic baseline levels of six isoflavones in blank plasma from rats consuming food containing dietary isoflavones were measured for the correction of the plasma concentrations. The principle pharmacokinetic parameters were calculated from rats with or without regular commercial food, and found to be altered by the dietary food containing some isoflavones.