The invention discloses healthy chili sauce and a preparation method thereof, and the healthy chili sauce is characterized by being prepared from the following raw materials by weight: 1-1.2 parts of rehmannia, 1.2-1.4 parts of flowers of pueraria, 1.1-1.3 parts of polygonatum, 1.3-1.5 parts of exocarpium citri rubrum, 0.9-1 part of fructu broussonetiae, 1-1.1 parts of lindernia ruellioides, 0.8-1 part of vitex root, 400-420 parts of rod chilli, 14-16 parts of pea, 6-7 parts of red yeast rice, 10-15 parts of white granulated sugar, 35-40 parts of salt, 22-25 parts of soy sauce, 13-14 parts of pine apple, 3-4 parts of fish roe, 40-45 parts of pork liver, 10-12 parts of mung bean starch, 15-17 parts of glutinous rice powder, 5-7 parts of oyster sauce, 10-12 parts of pork floss, 2-3 parts of cocoa powder, 15-20 parts of haw slices and 7-8 parts of a nutritional additive. The healthy chili sauce is fragrant, spicy and delicious, unique in flavor, and reasonable and scientific in formula, the added port liver is rich in vitamin A and trace elements of iron, zinc and copper, can improve eyesight and nourish blood, the glutinous rice powder is rich in proteins, vitamins, and nutrition; in addition, the healthy chili sauce is also added with a variety of Chinese herbal medicines, and can enrich blood, moisten, nourish stomach, moisten lung, improve eyesight, remove liver, regulate qi and activate blood circulation.