The essence of industrial structural optimization is now transforming from more input in the past to the dependence on informationization, the enhancement of independent innovation and being creative in macro-management to realize the industrial development. In order to solve the problems which was reflected during the course of the rapid development of Chinese pollution- free food industry , and the problems includes the product and scale structure of the enterprises which is the factor that affect the quality of the product , the key point is to disclose the general rules of industrial structure evolution and macro management innovation theoretically, to clarify the inherent basis of industrial structure optimization and how to adjust macro management to this requirement for developing China's pollution- free food industry. According to the theory of industry economy management, this paper systematically analyzes the industrial structure characteristics, problems and causes, and constructs the model of industrial structure optimization and upgrading. It also discloses the bases, conditions, the main contents and methods by way of the policy orientation for promoting industrial structure optimization of China's pollution- free food.