Experimental and theoretical investigations of the terahertz (THz) absorption spectra of two typical monosaccharides and disaccharides (D-glucose and lactose monohydrate), which have similar structures, were carried out by using terahertz time-domain spectroscopy (THz-TDS) and density functional theory (DFT). Firstly, the THz absorption spectra of D-glucose and lactose monohydrate were measured in the frequency range from 0.3 to 1.7 THz by THz-TDS system, and it was found that although the composition of lactose contained glucose, the THz-TDS was very sensitive to the structural changes of carbohydrates. The two carbohydrates showed their special THz fingerprint absorption characteristics in the measured THz band, respectively. Secondly, the vibration frequencies of these two carbohydrates in the THz band were calculated by using the DFT method, and the simulation results, including the unit cell configuration of D-glucose and the isolated-molecule and unit cell configuration of lactose monohydrate, were obtained. At the same time, combining molecular vibration animation displayed by GaussView and potential energy distributions (PED) analysis, the vibrational modes of these two carbohydrates in the THz band were assigned in detail. It was found that the vibrational modes of lactose monohydrate were closely related to the vibrational modes of hydroxyl (—OH), hydroxymethyl (—CH2OH) and glycosidic bond. The absorption peaks of D-glucose at 1.44 THz and lactose monohydrate at 1.38 THz were mainly caused by intermolecular interactions (hydrogen bonds and van der Waals forces), especially the strong hydrogen bonds. Finally, using the reduced density gradient (RDG) analysis, the type and intensity of the intermolecular interactions of D-glucose and lactose monohydrate were visualized. The experimental results indicated that the THz-TDS technique has a keen perception for the subtle changes in the structure of carbohydrates, which provides an effective method for investigation of intermolecular interactions and detection of carbohydrates.