The invention relates to soybean paste based on pre-fermentation and using Monascus purpureus as a dominant fungus symbiotic system, and a preparation method thereof, belonging to the technical fieldof seasoning preparation. According to the invention, soybeans are used as a raw material, three-stage fermentation is performed in virtue of a composite strain composed of Monascus purpureus TYQ017,Aspergillus oryzae 3.042, Actinomucor elegans, Aspergillus niger, Penicillium, Bacillus subtilis and Kluyveromyces marxianus, so the production of free amino acids is promoted, and the contents of aspartic acid, glutamic acid and threonine are increased; through combined usage of the Bacillus subtilis, the growth of dominant fungi is promote while the production of pathogens is inhibited; and through the introduction of the Kluyveromyces marxianus, the mellow flavor of the soybean paste is improved, and the soybean paste is allowed to be bright in color, soft and smooth in mouthfeel, rich in sauce flavor and delicious and lasting in aftertaste. The soybean paste is rich in monascorubin and lovastatin while retaining the nutrition of the soybean paste, has the effects of reducing cholesterol and preventing cardiovascular diseases; and the preparation method can improve productivity and shorten a production cycle, and has good social benefits.