Industry 4.0, also known as the Fourth Industrial Revolution, is characterized by process automation and digitization and the use of technologies such as the Internet of things, cloud, big data, artificial intelligence (AI), and embedded systems, among others. The application of automation technology based on Industry 4.0 contributes to the realization of a sustainable food security regime. Based on the policy guidance of the “No.1 Document” of the Chinese government on seed industry innovation and the quantitative analysis of the application, authorization, research, and development data of new varieties of agricultural plants in China in recent years, as well as the data of food import and export, this paper studies the risks and challenges facing China’s food security at present and explores the significance, existing problems, and specific countermeasures of resolving food security risks through seed industry innovation.