Heavy metals released by industry and transportation in daily life have a certain impact on the natural water environment. Microalgae, as the primary producer of the water environment is the first to be affected by lead. The subject tried to determine the degree of water pollution by studying the changes in the material composition of the algae. Traditional methods for studying biological macromolecules are complex and require the use of a large number of chemical reagents, so it is urgent to find new technology for the detection of microalgae substances. Terahertz and far-infrared technologies have high resolution, and the vibration frequencies of lipids, proteins and other substances are in the terahertz band, which provides a new technical means for studying the changes of microalgal matter. The terahertz and far-infrared spectroscopy was used to characterize the changes in biomacromolecules in S. obliquus cells under Pb stress. Fourier transform infrared spectrometer was used to collect the control group (0 mg·L^-1) and experimental group (0.5, 5, 20 mg·L^-1) Spectra of S. obliquus over time. Based on the characteristic absorption peaks of starch (9.1, 10.5, 17.2 THz) and carotenoids (16.7 THz), the starch content and carotenoid the change. At the same time, combined with chemometric methods, the principal component analysis was performed on the spectral data of 12 and 24 h stress time, which can easily distinguish the different experimental group samples of Pb stress from the control group. The results showed that under lead stress, the carbohydrate and carotenoid content in Scenedesmus obliquus gradually increased. Pb inhibits photosynthesis and affects the synthesis of polysaccharides and other macromolecules. The experimental results show that terahertz and far-infrared spectroscopy can be used as a fast and non-destructive method for the study of the changes in the composition of algae cells under lead stress, so as to determine the degree of water pollution.