Agriculture is the source of human food ingredients and the foundation for survival and development. Modern agriculture meets the demand for sufficient food, it has also led to diet-related diseases such as hyperlipidemia, hypertension, and hyperglycemia due to unbalanced diets. After the “Second International Conference on Nutrition (ICN2)” jointly held by the FAO and WTO in 2014, functional agriculture research aimed at meeting people's nutritional and health needs rapidly developed both domestically and internationally, China has issued guiding documents such as the “National Nutrition Plan (2017-2030)” and the “Healthy China 2030” planning outline. This paper systematically reviews the background of functional agriculture emergence and focuses on the functionalization of staple crops to discuss the research progress in functional agriculture of the world. It also summarizes the key research areas of functional agriculture, including exploration of functional components in germplasm resources, breeding of new functional varieties, agronomic enhancement measures, and development and promotion of health foods. On this basis, in accordance with the requirements of the “China Food and Nutrition Development Outline (2025-2030)” proposed by the Ministry of Agriculture and Rural Affairs, the National Health Commission, and the Ministry of Industry and Information Technology in February 2025, four suggestions are put forward: Strengthening top-level government design, establishing major projects for staple crop functionalization, accelerating the construction of standard systems, and improving intellectual property protection for varieties. These suggestions aim to provide theoretical support and practical paths for implementing China large-scale agriculture and grain strategy and ensuring national nutrition and health. This paper offers valuable insights for establishing a functional agricultural industry system with Chinese characteristics.