The present invention provides a fruit enzyme and a preparation method thereof. The fruit enzyme consists of the following raw material compositions in parts by weight: 20-25 parts of grapefruit skins, 15-25 parts of papaya, 10-20 parts of watermelon rinds, 10-15 parts of tomato skins, 10-15 parts of cucumber skins, 11-13 parts of wax gourd skins, 11-15 parts of kiwi fruit peels, 10-15 parts of wild strawberries, 7-11 parts of folium artemisiae argyi, 6-10 parts of mulberry leaves, 6-10 parts of rhododendron simsii, 5-10 parts of Hangzhou white chrysanthemum, 4-7 parts of citrus bigarradia white flower petals, 8-11 parts of olives and 20-30 parts of crystal sugar. The enzyme has a strong antioxidant activity, can help scavenge human body free radicals, and protects human body tissue cells from damages and injuries of the free radicals. When human body is exposed to sensitizing substances, the fruit enzyme can also play the anti-histamine effect, thus reduces or avoids the allergic reactions, can prevent the interference of allergic diseases, improves the human body immunity and enhances the body's anti-virus capabilities.