The invention discloses an automatic cleaning and disinfecting system for floating seedling-raising disks. The system comprises a frame, a conveying device, a cleaning device, a disinfecting device and a driving device, wherein the conveying device comprises a support rail, a transmission shaft, a chain wheel, two chains arranged in parallel and a disk pushing device arranged on the chains; the cleaning device comprises a cleaning brush, a pre-wetting pipe with a water outlet hole on the bottom surface, a flushing pipe and a rinsing pipe, and the pre-wetting pipe, the flushing pipe and the rinsing pipe are sequentially arranged on the frame from front to back; and the disinfecting device comprises a disinfecting box and a disinfecting pipe with the water outlet hole on the bottom surface. The automatic cleaning and disinfecting system can enable cleaning and disinfecting work to realize flow operation, complete cleaning and disinfection once, realize thorough cleaning, good disinfection effect, low breakage rate, fast cleaning speed and high efficiency, use water in a circulating manner and save water resources, and is portable, convenient and flexible; and furthermore, the automatic cleaning and disinfecting system is reasonable in design, easy to manufacture and simple to operate.