The research studied the best condition for protein purification in the wheat starch, for preparation of the wheat starch and the influence of the starch grain protein in the structure and properties when the starch is hydrolyzed. Firstly, we ensured the optimum condition for the Wheat protein purification by orthogonal test, at the same time, we obtained different protein content of wheat starch,the next step is to measure the protein content by the Kjedahl determination. Contrast between the SDS and protease in nitrogen function before setting-out the Enzymatic hydrolysis degree and the crystallinity in the starch samples of different nitrogen.It can be concluded from those experiments that compared with the SDS, the Protease is more effectively to remove the starch grain protein, which is useful to hydrolyze starch particles.