Since the chromatographic fingerprint was introduced, it has been accepted by many countries to assess the quality and authenticity of Chinese herbal medicine(CHM). However, solely using the chromatographic fingerprint to assay numerous chemicals is not suitable for the assessment of the whole internal quality and pharmacodynamics of CHM. Consequently, it is necessary to develop a rational approach to connecting the chromatographic fingerprint with effective components to assess the internal quality of CHM. For this purpose, a spectrum-effect relationship theory was proposed and accepted as a new method for the assessment of CHM because of its potential use to screen effective components from CHM. In this paper, we systematically reviewed the application of the spectrum-effect relationship theory in the research of CHM, including research mentality, different chromatographic analysis techniques, data processing technologies, and structure determination. Since the chromatographic fingerprint was introduced, it has been accepted by many countries to assess the quality and authenticity of Chinese herbal medicine (CHM). However, solely using the chromatographic fingerprint to assay multiple chemicals is not suitable for the assessment of the whole internal quality and pharmacodynamics of CHM. Therefore, it is necessary to develop a rational approach to connect the chromatographic fingerprint with effective components to assess the internal quality of CHM. For this purpose, a spectrum-effect relationship theory was proposed and accepted as a new method for the assessment of CHM because of potential use to screen effective components from CHM. In this paper, we systematically reviewed the application of the spectrum-effect relationship theory in the research of CHM, including research mentality, different chromatographic analysis techniques, data processing technologies , and structure determination.