Objective: To establish a liquid chromatography tandem mass spectrometry (HPLC-MS/MS) method to determine amygdalin and paeoniflorin in rat blood serum. Method: After protein precipitation by acetonitrile, a gradient elution procedure was performed to separate the samples by using acetonitrile and ammonium acetate buffer as the mobile phase. The quantitative determination was based on an HPLC-MS/MS in negative electron spray ionization mode and in multiple reaction monitoring (MRM) mode. The precursor to product ion transitions for amygdalin and paeoniflorin were 456.2 to 323.1 and 479.2 to 121.0, respectively. Results: The linear ranges of amygdalin and paeoniflorin were 1–300 ng/mL (rAmy = 0.9994，rPae = 0.9993) with the lowest limits of quantification were 0.3 ng/ml. The extract recovery of amygdalin and paeoniflorin were 91.1%, 94.2%, 92.0% and 90.3%, 93.7%, 94.1% at concentrations of 3, 20, 100 ng/mL, respectively. All the intra and inter day precisions of analysis were less than 15%, and the RE were in the range of ± 15%. Conclusion: The method is specific, sensitive, accurate, and suitable for determination of amygdalin and paeoniflorin in rat blood serum．