In recent years, with increasing attention to the health benefits of natural resources, food and medicinal substances—those possessing characteristics of both food and medicine—have become a research hotspot. These substances are widely used in traditional medicine and modern nutrition, and their bioactive components have shown great potential in regulating health. The development of target identification technologies has provided crucial support for elucidating the health-regulating mechanisms of food and medicinal substances. By utilizing cutting-edge technologies, such as biotinylated molecular probes and chemical proteomics, researchers could accurately identify the bioactive components in food and medicinal substances and their corresponding targets. The research that conducted in-depth analysis of nutritional components in food and their regulatory effects on health through chemical biology technologies formed a new interdisciplinary discipline:food nutrition chemistry and biology (FNChB). As an emerging interdisciplinary field, it integrated the theories and technologies of food science, nutrition, chemical biology, and molecular biology, offering new approaches and methods for exploring the functional factors and mechanisms of action in food and medicinal substances. The definition and characteristics of food and medicinal substances were systematically introduced, the principles and applications of target identification technologies were elaborated, and an in-depth analysis of the research progress on related targets and mechanisms was provided, aiming to offer new directions and theoretical support for the development and application of food and medicine substances.