The invention discloses a multifunctional high-flux automatic chromatography detector and applications thereof in the technical field of biomedical science. The chromatography detector includes a shell, a chromatographic system, a mechanical system, a detection system and an analysis system; the chromatographic system includes a chromatographic device and a chromatographic assembly; the side wallof the chromatographic device is provided with one or more channels, and the chromatographic assembly is installed in the channels; the mechanical system includes a pedestal, a motor, a photoelectricswitch and a clamping groove, wherein the clamping groove is used for installing the chromatographic device, and the photoelectric switch is used for locating the chromatographic assembly; the detection system includes a light source, a detector and a circuit board, and is used for capturing and detecting signals sent by the chromatographic assembly; the analysis system includes software and hardware equipment used for installing the software, and is used for the sorting, collecting, analyzing and storing the data; and the chromatography detector can be packaged by the shell. The chromatography detector can realize qualitative and quantitative detection based on the results of chromatography having principles of visible light, Raman, time-resolved fluorescence, fluorescence, chemiluminescence, up-conversion luminescence, etc.