The invention discloses a method for removing bacterial contamination in fungi. The method comprises the following steps: (1) carrying out high temperature sterilization on a prepared fungus culture medium, pouring the sterilized fungus culture medium into a sterile culture dish, and cutting one or more than one small hole on a culture medium flat plate after the culture medium is solidified; (2)selecting samples in proper size and placing the samples in the small hole; (3) covering a sterile cover glass, and slightly pressing the periphery of the cover glass to make the cover glass closely contact with the culture medium so as to ensure that no air bubbles are left between the culture medium and the cover glass; (4) putting the culture medium obtained in the step (3) into a constant temperature and humidity incubator for culture; and (5) picking new fungus hyphae growing around the cover glass, and re-inoculating the fungus hyphae to a new fungus culture medium for culture, thereby obtaining fungus colonies. The invention has the advantages of excellent bacteria removing effect, no rebound, wide applicability, simple operation, small workload and short experimental period.