In designing a supply chain, product structure has been proved to be an important factor affecting supply chain quality control level decision of the buyers and the suppliers. In this article, product structure is divided into separable and non-separable sorts. And then principal agent models for them are set up accordingly. Classic control theory is used to solve the models. Results under different product structures are compared. Under non-separable product structure, the buyer's decision on quality evaluation level is higher than that under separable product structure, and correspondingly the buyer's income is higher. And the effect of product structure on supply chain quality control decision is analyzed. At last simulation calculation is done.