Based on the BERTopic model, this study analyzes 15,744 scientific papers in the field of functional agriculture from 1995 to 2024 to uncover core themes and evolutionary trends in global functional agriculture, and particularly focuses on revealing the developmental trajectory in China. The results indicate that global functional agriculture research is characterized by diverse themes and intensive study, forming a multi-topic cross-network centered on plant chemical extraction and agricultural soil research, with a focus on food nutrition, human health, and environmental protection. By contrast, China’s functional agriculture research demonstrates a more focused and in-depth approach, concentrating on functional food development and agricultural environmental protection themes, with notable growth trends in areas such as selenium-enriched products and resistant starch. Combined with China’s agricultural development environment, this study makes the following suggestions for the development of functional agriculture in China: (1) Promoting interdisciplinary cooperation between functional agriculture and other technologies. (2) Developing agricultural products with Chinese characteristics and forming Chinese functional agricultural product brands. (3) Utilizing smart farming technology to boost functional agriculture.