The invention discloses a medical instrument cleaning device. The medical instrument cleaning device comprises a cleaning table, a filtration tank and a water storage tank; a faucet is installed on the cleaning table and connected with a cleaning tank, and a water outlet pipe is connected with the bottom of the cleaning tank. The water outlet pipe is communicated with a water inlet pipe of the filtration tank, the water inlet pipe of the filtration tank is connected with a flow guide hole, a first filtration screen is installed on the bottom of the flow guide hole, and a water inlet bucket isarranged on the lower side of the first filtration screen and communicated with a filter element device which is connected with a water outlet bucket. A second filter screen is arranged on the bottomof the water outlet bucket and installed above a flow outlet which is connected with the water storage tank through a water outlet pipe of the filtration tank, a water inlet pipe of the water storagetank is installed on the bottom of the water storage tank, the water inlet pipe of the water storage tank is provided with a water inlet valve which is movably connected with a floating ball connection rod, and a floating ball is fixedly hung on the floating ball connection rod. According to the medical instrument cleaning device, by arranging the filtration tank, the water storage tank and a water supply device, water for medical instruments can be recycled, environmental protection is facilitated, and a disease prevention effect is easily achieved.