The present invention provides a production-line-type high-throughput screening system, which relates to the field of biotechnology and testing equipment. The system comprises of four manipulators, three parallel conveyor belts with fixed slots, 2-DOF slipway and fixed fixtures, 96-channel pipetting system, coloring device, oscillating mixing device, microplate reader, well plates loading platform and well plates recycling platform. Manual operation takes five minutes to detect one 96-well plate, while this system can handle 20 96-well plates per minute. It expands the number of screening targets, making the screening process more clearly and concisely and liberating manual labor. The system makes effective contributions to the development of microbial breeding technology.