The invention provides a high-throughput screening system based on multi-manipulators, and belongs to the field of biotechnology and detection equipment. A high-throughput screening system based on multi-manipulators, comprises of the first manipulator, sampler, pipette, plate washer, microplate reader, the second manipulator, centrifuge, deep-well plate library, waste shallow-well plate barrel, shallow-well plate library, waste needle plate barrel, needle library, waste deep-well plate barrel, collection box. The present invention is a combination of microbiology and mechanics. The aim of the invention is to realize the automation and intelligentization of the high throughput screening experiment, effectively improve the experimental accuracy, reliability and efficiency. It contributes to the development of high throughput screening technology for microorganisms and drugs.