A method for the simultaneous analysis of pesticide multiresidues in three root/rhizome-based herbal medicines (Cnidium officinale,Rehmannia glutinosa, andPaeonia lactiflora) was developed with GC-MS/MS. To determine the concentrations of pesticide residues, 5 g of dried samples were saturated with distilled water, extracted with 10 mL of 0.1% formic acid in acetonitrile/ethyl acetate (7:3, v/v), and then partitioned using magnesium sulfate and sodium chloride. The organic layer was purified with Oasis PRiME HLB plus light, followed by a cleanup with dispersive solid-phase extraction containing alumina. The sample was then injected into GC-MS/MS (2 μL) using a pulsed injection mode at 15 psi and analyzed using multiple reaction monitoring (MRM) modes. The limit of quantitation for the 296 target pesticides was within 0.002–0.05 mg/kg. Among them, 77.7–88.5% showed recoveries between 70% and 120% with relative standard deviations (RSDs) ≤20% at fortified levels of 0.01, and 0.05 mg/kg. The analytical method was successfully applied to real herbal samples obtained from commercial markets, and 10 pesticides were quantitatively determined from these samples.