The clean production process of separating soybean protein features the utilization of waste produced in the production process as resource. Waste water is processed comprehensively and utilized circularly to obtain soybean oligosaccharide, whey protein and isoflavone. Soybean coat and soybean residue are used in producing diet fiber. Soybean plumule is used in producing soybean saponin, plumule oil and plumule protein, and the oil residue is used in producing phospholipid. The present invention can solve the problem of waste water and water sludge pollution while producing several functional food materials.