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The protease that the Bacillus subtilis produces hydrolyzed defatted soy flour,the best hydrolytic parameter-pH value 6.5,temperature32 ℃,concentration of substrate12%,inoculum size 8%,time 30h was confirmed. The peptides mixture was separated by ultrafiltration membrane,the optimum condition was:temperature40℃、content 4%、pressure0.25Mpa、pH value 7.The vitro digestion test、determination of amino acid and molecular weight、electron microscopic observation were studied about defatted soy flour、protein isolate、ultrafiltration soybean protease hydrolysate and the uncleared.