A medical instrument sterilization method is disclosed, which characterizes in following process: pending medical instrument for sterilization treatment being placed in a closed container, then being vacuum pumped, the vacuum pressure of the container being controlled between 1 Pa to 1500 Pa, air and/or oxygen and/or inert gases are charged to closed container and the vacuum pressure being between 1 Pa to 1500 Pa, microwave is fed, the favorable power of which should make the gas charged into the container to generate ionization, the microwave be cut after the sterilization, then air being charged to release vacuum to finish the whole process.