Searching for bioactive compounds from natural resources such as plant materials has become a focus for study. Several models, such as animal (biofluid, organ and tissue) and cellular (several kinds of cell lines), have traditionally been used for this purpose. As a fast, economic and effective way to identify or predict bioactive compounds in complex matrices, biochromatography has developed rapidly during the past years. Combing the properties of traditional chromatography and biomaterials, biochromatographic analysis possesses features of simultaneous screening, separation and structural identification for active compounds in a complex matrix. According to the process, biochromatography can be divided into offline and online approaches. For offline bioextraction, the biomaterials are used as the extraction phase and followed by routine chromatographic analysis. For online biochromatography, the biomaterials are directly used as the stationary phase for chromatographic analysis. This paper reviews the applications of offline bioextraction followed by chromatographic analysis and online biochromatography, including molecular, cell membrane and cell, and artificial biomembrane chromatography in the screening or predicting active compounds from natural sources.