The invention discloses a multi-purpose medical instrument internal structure disinfection machine, which includes a box body, an ozone generator connected with a positive pressure air pump, a negative pressure air pump and a control circuit are arranged in the box body, the ozone generator is connected with the first The negative pressure air pump is connected to the filter through the second conduit, the atomizer is arranged in the box, the atomizer is connected to the first conduit through the third conduit, and the control circuit controls the positive Compression pump, ozone generator, atomizer and negative pressure air pump are opened or closed, and described atomizer is provided with the hydrogen peroxide aqueous solution that volume percent concentration is 8%~12%, and the present invention is applied to various Disinfection of the inside of pipeline medical equipment, such as ventilator, anesthesia machine, lung function tester, extracorporeal circulation machine, artificial kidney dialysis machine, it can completely disinfect the inside of the contaminated instrument without being corroded or damaged.