The present paper firstly reviewed the research progress and main methods of NIR spectral assignment coupled with our research results. Principal component analysis was focused on characteristic signal extraction to reflect spectral differences. Partial least squares method was concerned with variable selection to discover characteristic absorption band. Two-dimensional correlation spectroscopy was mainly adopted for spectral assignment. Autocorrelation peaks were obtained from spectral changes, which were disturbed by external factors, such as concentration, temperature and pressure. Density functional theory was used to calculate energy from substance structure to establish the relationship between molecular energy and spectra change. Based on the above reviewed method, taking a NIR spectral assignment of chlorogenic acid as example, a reliable spectral assignment for critical quality attributes of Chinese materia medica (CMM) was established using deuterium technology and spectral variable selection. The result demonstrated the assignment consistency according to spectral features of different concentrations of chlorogenic acid and variable selection region of on-line NIR model in extract process. Although spectral assignment was initial using an active pharmaceutical ingredient, it is meaningful to look forward to the futurity of the complex components in CMM. Therefore, it provided methodology for NIR spectral assignment of critical quality attributes in CMM.