Terahertz (THz), as an advanced spectral technology, has unique absorption characteristics for most biological macromolecules. In this work, the theoretical fundamentals for the application of THz time-domain spectroscopy (THz-TDS) to molecular characterization and fingerprint peak detection of three plant growth regulators (PGRs), including 2,4-Dichlorophenoxyacetic acid (2,4-D), forchlorfenuron (CPPU) and indole-3-acetic acid (IAA) were researched. Meanwhile, the effects of eight types of window functions on THz spectra were studied when converting time-domain spectra into frequency-domain spectra by Fourier transform. Based on the optimal window function, the THz absorption coefficient and refractive index of PGRs in frequencies of 0.2-3 THz were extracted. The molecule structure and vibration mode of three PGR samples were simulated by using density functional theory (DFT). The results showed that the three PGRs had different fingerprint peaks. Characteristic absorption and anomalous dispersion of 2,4-D were found at 1.35, 1.57 and 2.67 THz, those of CPPU were found at 1.77 and 2.44 THz, and the absorption peak of IAA was located at 2.5 THz. The absorption peaks obtained from THz spectra were identified according to the theoretical calculation results of DFT. These fingerprint peaks in THz spectra were generated by the interior stretching vibration and external deformation vibration of molecular groups. The experimental results revealed the feasibility of identifying PGRs species and detecting residues using THz-TDS.