The terahertz (THz) multivariate spectral characteristics and the molecular dynamics of three pyrethroid pesticides, including deltamethrin, fenvalerate, and beta-cypermethrin, were studied in this paper. THz spectra of the pesticides were measured in frequency range of 0.06–3.5 THz by using THz time-domain spectroscopy (THz-TDS). To improve the THz spectral quality, the wavelet threshold de-noising (WTD) method was used to remove spectral noise and the spectral baseline correction (SBC) method was used to remove baseline drift. Specific absorption peaks were observed in the processed THz spectra of the three pesticides. Deltamethrin showed three peaks at 0.90, 1.49, and 2.32 THz. Fenvalerate had five peaks at 1.13, 1.43, 1.61, 1.98, and 2.58 THz. Beta cypermethrin had four peaks at 1.27, 1.84, 2.12, and 2.92 THz. The density functional theory (DFT) was used to characterize the molecular dynamics and formation mechanism of the absorption peaks. Results showed that there was a good matching effect between the THz experimental spectra and the DFT quantum calculation spectra. Based on the characterized fingerprint absorption peaks, the linear addition model was used to simulate the THz spectra of mixed pesticides. The simulated spectra of multicomponent pesticides were demonstrated to be in good agreement with those obtained by THz-TDS. By analyzing the absorption peaks of THz spectra, the composition and concentration of multicomponent pesticides could be determined. The proposed strategy presented an analytical methodology for studying the THz spectral characteristics of pesticides. In addition, this work provided experimental and theoretical basis for the detection potential of pesticides in agricultural products based on THz technology.