This paper takes two isomers of sugars [D-(+)-glucose and D-(-)-fructose] as the research object. Firstly, the terahertz time domain spectroscopy system was used to obtain the characteristic absorption spectra of the two isomers in the band of 0.4--1.9 THz. The two different absorption peaks at 1.43 THz and 1.64 THz can be used for qualitative identification. Secondly, in order to further explore the formation mechanism of absorption peaks, the density functional theory was used to optimize the cell structure and identify the vibration modes. Finally, the types, locations, and intensities of the weak intermolecular interactions between glucose and fructose cells were visualized by the reduced density gradient and independent gradient model. The research results show that the characteristic absorption peaks of the two substances in the terahertz band are mainly derived from the collective vibration mode caused by the hydrogen bond interaction between the functional groups of the two molecules. This study provides valuable experimental and theoretical references for the qualitative detection of the isomers of sugars and precise quantitative analysis, as well as the formation mechanism of terahertz absorption peaks of D-(+)-glucose and D-(-)-fructose.