The invention discloses a high-throughput device for detecting peri-implantitis flora. The device comprises a high-throughput box, a sliding door and a controller, wherein the sliding door and the controller are placed on the left side and the right side of the high-throughput box respectively, the sliding door is connected with the high-throughput box through sliding rails in a sliding mode, thecontroller is detachably connected with the high-throughput box through bolts, the high-throughput box is internally provided with a workbench, a thermometer and a hygrometer, the workbench is horizontally placed on the bottom of the high-throughput box, a photometer, a centrifugal machine and a DNA extraction device are arranged on the upper part of the workbench, the photometer, the centrifugalmachine and the DNA extraction device are horizontally placed on the surface of the workbench, and the workbench is internally provided with a liquid treatment device and a sterile storage chamber. According to the high-throughput device for detecting the peri-implantitis flora, by adopting a biochip high-throughput technology, change of protein and genes of body fluid of saliva or gingival crevicular fluid or the like of a tooth implantation patient can be detected, and the susceptibility of the patient to peri-implantitis is identified.