The invention discloses ginkgo biloba soybean paste and a preparation method thereof. The ginkgo biloba soybean paste is prepared from the following raw materials in parts by weight: 50-100 parts of soybeans, 40-80 parts of ginkgo biloba, 10-20 parts of flour, 0.6-0.9 part of aspergillus oryzae, 0-0.3 part of aspergillus niger, 8-16 parts of table salt, 15-30 parts of chilies, 8-16 parts of white granulated sugar and 0.3-0.6 part of xanthan gum. According to the soybean paste disclosed by the invention, the content of the ginkgo biloba is high, ginkgo biloba fruits contain active ingredients such as flavone, lactone, white tartaric acid, ginkgol, bilobol, bacteriostatic proteins and polysaccharide, and the soybean paste has the effects of inhibiting fungi, improving brain functions, resisting anoxia, resisting fatigue, delaying senescence and the like, and has very high nutritional value. The ginkgo biloba soybean paste is ruddy in color and luster, rich in sauce fragrance, obvious in delicate flavor, palatable in salty and sweet taste, moderate in thickness and free of impurity particles, and development of the ginkgo biloba soybean paste can enrich the variety of thick broad-bean paste and open up a new way for deep processing of the ginkgo biloba. The preparation method is simple in process and low in cost.