A rapid, sensitive and selective ultra high-performance liquid chromatography-tandem mass spectrometry UHPLC–MS/MS method has been developed and validated for the simultaneous determination of fourteen bioactive ingredients (gallic acid, geniposidic acid, protocatechuic acid, caffeic acid, ferulic acid, scopoletin, apigenin-7-o-glucuronide, daidzein, apigenin, ursolic acid, oleanolic acid, β-sitosterol, coniferin, and stigmasterol) in the plasma and tissues of rats. Danshensu and icariin were used as internal standards (IS1 and IS2). The chromatographic separation was achieved by using an Agilent ZORBAX RRHD Eclipse Plus C18 column (2.1 mm × 50 mm, 1.8 μm) with gradient elution using mobile phase, which consisted of 0.1% acetic acid water (solvent A) and methanol (solvent B) and pumped at a flow rate of 0.3 mL/min. Mass spectrometric detection was performed in multiple reaction monitoring (MRM) mode utilizing electrospray ionization (ESI) in positive and negative mode. The plasma samples were pretreated via protein precipitation with 300 μL of methanol containing 0.1% (v/v) formic acid and organ homogenates were processed by solid-phase extraction (SPE) with Waters Oasis HLB 3 cc (60 mg), respectively. The intra- and inter- day precisions (RSD%) were less than 10.3%, while the accuracy was ranged from –7.34% to 9.10%. Extraction recovery ranged from 85.02 to 112.0% and the matrix effects ranged from 85.12% to 109.6%. The present method exhibited excellent linearity and the lower limits of quantification (LLOQ) were 30.0 ng/mL, 15.0 ng/mL, 80.0 ng/mL, 30.0 ng/mL, 10.0 ng/mL, 3.0 ng/mL, 2.5 ng/mL, 2.5 ng/mL, 1.5 ng/mL, 15.0 ng/mL, 75.0 ng/mL, 15.0 ng/mL, 30.0 ng/mL, and 20.0 ng/mL for gallic acid, protocatechuic acid, geniposidic acid, caffeic acid, ferulic acid, scopoletin, apigenin-7-o-glucuronide, daidzein, apigenin, ursolic acid, oleanolic acid, β-sitosterol, coniferin, and stigmasterol, respectively. This analytical method was verified by the FDA guidelines for bioanalytical method validation and applied to investigate the pharmacokinetics and biodistribution of fourteen constituents of Hedyotis diffusa Willd extract in rats. These results provide useful information for improving the pharmacokinetics and biodistribution of fourteen bioactive ingredients of Hedyotis diffusa Willd extract in SD rats, supporting additional clinical application and Chinese herbal medicine safety evaluations.