Near infrared (NIR) assignment of Isopsoralen was performed using deuterated chloroform solvent and two-dimensional correlation spectroscopy (2D-COS) technology. Yunkang Oral Liquid was applied to study Isopsoralen, the characteristic bands by spectral assignment as well as the bands by interval partial least squares (iPLS) and synergy interval partial least squares (siPLS) were used to establish partial least squares (PLS) model. The coefficient of determination in calibration (R2cal) were 0.9987, 0.9970 and 0.9982. The coefficient of determination in cross validation (R2val) were 0.9985, 0.9921 and 0.9982. The coefficient of determination in prediction(R2pre) were 0.9987, 0.9955 and 0.9988. The root mean square error of calibration (RMSEC) were 0.27, 0.40 and 0.31 ppm. The root mean square error of cross validation (RMSECV) were 0.30, 0.67 and 0.32 ppm. The root mean square error of prediction (RMSEP) were 0.23, 0.43 and 0.22 ppm. The residual predictive deviation (RPD) were 31.00, 16.58 and 32.41. It turned out that the characteristic bands by spectral assignment had the same results with the chemometrics methods in PLS model. It provided guidance for NIR spectral assignment of chemical compositions in Chinese Materia Medica (CMM).