The invention discloses a method for increasing Clostridium kluyveri fermentation based hexanoic acid production yield by soybean residues being a soybean product processing byproduct. The method includes: (1) preparation of soybean residue actinomucor elegans culture, to be more specific, performing inoculation of actinomucor elegans in a soybean residue culture medium conical flask, statically culturing, drying obtained culture, and grinding into powder to obtain the soybean residue actinomucor elegans culture; (2) clostridium kluyveri seed culture; (3) hexanoic acid fermentation culture, to be more specific, performing inoculation of clostridium kluyveri seed liquid in a hexanoic acid fermentation culture medium, and adding the soybean residue actinomucor elegans culture in a fermentation culture process. The method is evident in increasing of clostridium kluyveri based hexanoic acid yield, has advantages of simplicity in operation, production cost reduction, pollution treatment reduction and the like and is easy for industrial application.