The invention discloses a novel polyhedral multi-channel high-throughput chromatographic device and application thereof. The device is of a polyhedral structure; the main part of the device is a shell; the device may further have a top cover and a pedestal; and the shell is filled with a drying agent, and the bottom and the top of the device are connected with stepping equipment. The device can realize multi-channel vertical ascending or descending chromatography and perform high-throughput parallel detection and analysis of a plurality of marker molecules on one or more clinical or non-clinical samples at the same time; the device can realize automatic or semi-automatic, qualitative and quantitative analysis with the naked eye in the aid of automatic sample loading, spectroscopic or electromagnetic wave spectrometers and analytical assemblies; target objects to be detected may be biomacromolecules and small-molecular compounds like proteins, nucleic acids and sugars and may be cellular and subcellular components and the like; so the device is applicable to fields like clinical diagnosis, inspection and quarantine, food safety testing, judicial expertise and drug detection. The device is simple to operate, convenient to carry and capable of significantly improving detection efficiency and reducing sample amount.