Although enzyme-assisted aqueous extraction processing (EAEP) is an environmentally friendly alternative technology to hexane extraction of soybean oil，it’s application is limited by enzyme price. This processing employs microbial fermentation to extract oil and protein from a variety of pretreatment full fat soy flours, and optimizes the fermentation conditions using the Response Surface Methodology (RSM). The results showed that extrusion combination with wet- thermal treatment were beneficial to improving oil and protein extraction, and total oil extraction yield achieve the highest value 95.1% at 7.4% extruded full fat soy flour, 5.4% inoculation volume, the initial pH8.4. At this condition, protein extraction yield reached to 86.1%. These advances make the microbial fermentation extraction processing attractive channel as the front-end of a soybean biorefinery.