This paper introduces the importance of innovation system for agricultural products processing industry. Based on the principles of openness, dynamics, systematization, outstanding industrial characteristics and close cooperation, a diversified agro-processing innovation system is constructed. It is an innovation subject system of agricultural products processing industry which takes agricultural products processing industry as the core, independent innovation as the center, and university, scientific research institution, government, intermediary organization, financial institution and peasant as the supplements. It is also an innovation operation system of agricultural products processing industry which consists of knowledge innovation, technological innovation, knowledge propagation and application. These 4 subsystems are analyzed based on guaranteeing the basic position of agricultural products processing industry in development system, which are technology innovation extension of agricultural products processing industry, system guarantee in innovation system of agricultural products processing industry, knowledge propagation taking university as the core, and innovation service of agricultural products processing industry adapted to the law of market. Measures for innovation system of agricultural products processing industry in these 4 subsystems are also pointed out.