A specific and selective UPLC-MS/MS method was developed and validated for the simultaneous determination of isoflavonoids(3'-hydroxy puerarin, puerarin, daidzin, daidzein, genistin, genistein), flavonoids (baicalin, baicalein, wogonoside, wogonin, liquiritin)and alkaloids(berberine, jatrorrhizine, palmatine)(14 bioactive compounds) of Gegen Qinlian Decoction(GQD) in plasma. The pharmacokinetics characteristics of 14 bioactive compounds were study after oral administration of GQD at a single dose to rats. Prednisolone was used as the internal standard of liquiritin, and naringin was used as the internal standard of the other thirteen analytes. After the plasma samples were processed by precipitation protein method, the constituents and internal standards were gradient eluted by using a Zorbax SB-18 column with a mobile phase of acetonitrile(A) and 0.1% formic acid aqueous solution(B) using a gradient elution of 0-2.5 min, 15%-30% A; 2.5-3.5 min, 30%-35% A; 3.5-5.0 min, 35%-40% A; 5.0-9.0 min, 40%-60% A; 9.0-11.0 min, 60%-15% A, and the flow rate was 0.4 mL·min⁻¹. The auto sampler was conditioned at 25 °C and the sample injection volume was 5 μL. A mass spectrometry was applied with electrospray ionization (ESI) ion source in the positive and negative ion multiple reaction monitoring(MRM) mode. All pharmacokinetic parameters were processed by non-compartmental analysis with DAS 3.2.2 software. The results showed that the linear correlation coefficient of the 14 components were all greater than 0.99, indicating that the method had good linearity in their respective concentration ranges. Post-preparative stability (25 °C, 24 h), short-term stability(25 °C, 12 h), long-term stability (-20 °C, 7 d), and freeze and thaw stability (3-cycles) of the fourteen constituents were examined to evaluate the stability of methodology. The results of the inner and inter-day relative standard deviations were both less than 10%, indicating legitimate precise and accuracy to the requirement of biological sample analysis. The assay method is proved to be sensitive, accurate and convenient. It can be applied to the pharmacokinetic study of the fourteen analytes. The kinetic parameters of the related drugs were calculated according to the blood concentration of the 14 components. The results showed that the MRT0-t of the isoflavones and flavonoids was 7.5-11.8 h, T1/2z were mainly in 11.0-29.7 h, and the AUC0-t flavonoids were larger than the isoflavones. The MRT0-t of alkaloids were between 4.3-7.2 h, T1/2z were 1.0-5.0 h, AUC0-t were less than flavonoids and isoflavones. The results suggest that flavonoids and isoflavones have a high concentration of blood and long time of action, which are beneficial to the anti-inflammatory and antipyretic effects. The concentration of alkaloids in the body is low and the time of action is short, and it may play its bacteriostasis in the intestinal tract.