The invention discloses a natural fungicide for preventing and treating peach scab and a preparation method thereof. The natural fungicide is prepared by ultrasonically mixing, by weight, 6-10 parts of berberine extract, 1-5 parts of sedum sarmentosum extract, anti-freezing solution glycerinum, preservative ethyl alcohol and water. In the natural fungicide, the content of berberine is 5%. The preparation method comprises the following steps that 1, the sedum sarmentosum extract is extracted; 2, the berberine extract is extracted; 3, the berberine extract and the sedum sarmentosum extract are mixed in proportion, and the anti-freezing solution glycerinum, the preservative ethyl alcohol and the water are added into the mixture to ultrasonically prepare the fungicide. The natural fungicide for preventing and treating peach scab is wide in raw material source and low in cost, is prepared from pure natural raw materials, and is nontoxic, free of pollution and capable of effectively preventing and treating peach scab.