Soybean molasses is the by-product of the production of concentrated proteins in soybeans. It is a kind of brown sticky pulp thing after the concentration of extract liquor by the ethanol of defatted soybean meal. Soybean molasses contains a variety of functional components. It mainly includes soybean oligosaccharides, soybean isoflavone, and other physiologically active components, which have many beneficial effects on the human health. By using monosaccharides and polysaccharides with the method of fermentation, the concentration of functional polysaccharides is improved and the purpose of purifying glycogen is achieved. One strain of yeast, that is, Saccharomyces cerevisiae C that has the function of high consumption to sucrose, and high retention rate to stachyose and raffinose is screened from four stains of yeast and one strain of lactobacillus. The optimal condition for the fermentation of soybean molasses is initial molasses sugar concentration of 9%, initial pH value of 6.5, inoculation amount of 3% and fermentation at 30℃ for 24h. The retention rates in hydrolysates of soybean molasses are 0% for sucrose, 60.90% for functional oligosaccharide, and 24.46% for glucose and fructose. And repeat stability reaches at 95% under the optimal fermentation condition.