The invention discloses a preparing method of whitebait fishpaste acid. The preparing method comprises the following steps: firstly salting whitebaits, then preparing sticky rice sweet wine, finally mixing the salted whitebaits, zao peppers and the sticky rice sweet wine in a proportion, sealing and fermenting to obtain the whitebait fishpaste acid. The whitebait fishpaste acid is same as or superior to traditional fishpaste acid in the aspects of color, texture, flavor, and nutrition and the like, and the main nutrient contents of the whitebait fishpaste acid, such as total acid, reducing sugar, total sugar, protein, fat and the like, are not obviously different from those of the traditional fishpaste acid; heavy metals such as Hg, Pb, Cd, As, Sn and the like are not detected in the whitebait fishpaste acid, the contents of Ca and Zn are higher, the contents of Cu and nitrite are respectively 1.281mg / Kg and 0.125mg / Kg, both far lower than corresponding national health and safety standards; and the preparing method provided by the invention solves the problem of limitation of key raw materials in traditional fishpaste acid processing, protects and inherits the traditional cooking culture of the Miao nationality and traditional fermentation food fishpaste acid.