Continuous cropping obstacle is the greatest difficulty in Rehmannia glutinosa planting. It must be replanted after 8～10 years. However, the mechanism of the continuous cropping obstacles is not clear yet. An analytical method based on Fourier transform infrared spectroscopy (FTIR-ATR) and Two-Dimensional Infrared Correlation Spectroscopy (2D-IR) is proposed. Collected from the main crop (YA-One), second crop (YA-Two), 10-year-old interval (YA-Ten) and blank (CK) of the spectra of four kinds of Rehmannia glutinos soil samples. Norris noise filtering and smoothing, second derivative and two-dimensional correlation spectrum analysis were performed to extract characteristic spectra, analyzed the fingerprint of compounds in the soil. The results showed that the peaks of different continuous cropping soils were similar, and the main characteristic absorption peaks of spectra were around 3 621, 3 439, 2 932, 2 860, 2 513, 1 798, 1 636, 1 433, 1 029, 887, 783, 695, 546 and 469 cm-1. Compared with CK, the absorption intensity of YA-Two is the strongest, and these absorption peaks mostly represent the functional groups such as hydroxy -OH, carbonyl CO, C-O, and substituted absorption of the benzene ring in phenolic acids, indicating the accumulation of phenolic acids in Rehmannia glutinos in continuous cropping. The reverse stretching vibration and symmetric stretching vibration of saturated methylene CH2 in the glycosides were observed At t 2 925 and 2 857 cm-1. The absorption intensity of Ya-Two was the smallest, and Ya-Ten was the largest. The results indicated that the glucoside components decreased in continuous cropping soil. The position, number and strength of automatic peak and cross peak were different in the two-dimensional infrared correlation spectra of the soil of Rehmannia glutinos in bands 920～1 750, 1 490～1 710 and 1 500～1 548 cm-1, which clearly showed the difference of functional groups. The results showed that the rapid detection of organic compounds in soil could be achieved by using Fourier transform infrared spectroscopy (FTIR) and two-dimensional infrared correlation spectroscopy (TD-IR), which provided a theoretical basis for studying Rehmannia glutinos continuous cropping obstacles.