Although hexane extraction of soybean oil has the high recovery，residual hexane in oil is noxious for consumer health. Crew pressing and extruding-expelling extraction processes denature protein to render functional properties poor for food and meal use. This processing employed microbial fermentation to extract protein from full fat soy flour so that denaturation degree of protein reduced. The results showed that low temperature flaking and extrusing soy flakes was beneficial to improving protein extraction, after optimizing the fermentation conditions with the Response Surface Methodology (RSM), total protein extraction yield achieved the highest value - 86.66% at optimal fermentation conditions - 6.6% extruded full fat soy flour, 5.4% inoculation volume, the initial pH8.1. These advances make the microbial fermentation extraction process of protein from soybeans attractive channel as the environmentally – friendly technology.