The invention discloses a special sauce for Sichuan cuisine and a preparation method thereof. According to a formula, the sauce comprises the following raw materials in parts by weight: 100 parts of koji, 1.5-2.0 parts of seed koji and 75-85 parts of water, wherein the koji comprises 11-13 parts of patent flour, 3-5 parts of soybean meal, 1-2 parts of wheat bran powder and 1.5-2 parts of water, and the seed koji comprises 4-6 parts of aspergillus oryzae, 2-3 parts of aspergillus niger and 1 part of rhizopus; the preparation method comprises the following steps: raw material pretreatment, seedkoji preparation, koji preparation, fermentation, sterilization and packaging; according to the invention, a split brewing process of medium-temperature quick brewing and high-temperature aging brewing is adopted, and the sauce is fermented with the temperature and the humidity under the control of a solar greenhouse intelligent control system; the sauce has the characteristics of strong flavor, high chroma and high freshness, and can be used in processing of Sichuan cuisine, such as used in the processing of Sichuan sausage; partial or all nitrite is replaced by the sauce, so that a product is ruddy in color, low-nitrate or nitrate-free products can be produced, and at the same time, the sauce has the function of enhancing the flavor of products.