A cleaning and disinfecting apparatus for medical instruments is provided. The apparatus comprises a cleaning and disinfecting box, a washing device, an atomization disinfection device, a steam sterilization device and a waste liquid collecting box. The upper end of the cleaning and disinfecting box is connected to the atomization disinfection device, the left end of the cleaning and disinfecting box is connected to the washing device, the right end of the cleaning and disinfecting box is connected to the steam sterilization device, and the lower end of the cleaning and disinfecting box is connected to the waste liquid collecting box through a right liquid discharging pipe and a left liquid discharging pipe. The atomization disinfection device comprises a disinfectant storing box, a liquid discharging pipe, a pressure pump and an atomization device, wherein the disinfectant storing box is connected to the atomization device through the liquid discharging pipe, the pressure pump is disposed at the liquid discharging pipe, and the atomization device is disposed in the cleaning and disinfecting box. The washing device comprises a water tank, a heating device, a water supplying pipe, a pressure pump, a filter drum and a spraying device. The spraying device comprises a spraying pipe and spraying nozzles. The steam sterilization device comprises a heating device, a heating water tank, a steam chamber and a steam conveying pipe. The apparatus performs disinfection and sterilization by adopting a three-level sterilization manner and is good in sterilization effects and high in efficiency.