The invention relates to a disinfection system for medical examination instruments based on an intelligent algorithm. The system comprises a disinfection bin, an ultraviolet lamp, a first visual collector, a heating wire, a first temperature detector, a first conveyor belt, a disinfectant recovery tank, a disinfectant storage tank, a nozzle, a drying bin, a second visual collector, a fan, a drying pipe, a heater, a second conveyor belt, a fan and a central control unit. According to the system, the independent bins are used for disinfecting and drying the appliances respectively, the situation of incomplete disinfection can be avoided, so that the situation of secondary infection or cross infection generated when the appliances are used is effectively avoided, and the disinfection efficiency of the system on the appliances is effectively improved. Meanwhile, whether a spray head uniformly sprays the disinfectant on the surface of the appliance or not is judged by using the average distribution density of the disinfectant drops, so that whether the disinfection on the surface of the appliance is completed or not is quickly judged, and the disinfection efficiency of the system on the appliance can be further improved.