Plant-based foods play a vital role in a healthy dietary structure for residents and serve as significant sources of the three major nutrients, dietary fiber, various vitamins, and minerals. With the improvement of living standards, people's pursuit of food has upgraded from “filling” to “eating well”. Accordingly, the flavor of foods (including plant-based foods) has become a key factor affecting consumer preferences. Especially, the concept of “biological flavor formation” under the action of biological media such as enzymes and microorganisms is gaining more and more attention and recognition from consumers. Food flavor produced by biological media such as enzymes and microorganisms is in line with consumers' expectation of natural, safe, non-additive or less additive food, so it is increasingly favored. Therefore, it is of great significance to understand the biological flavor formation mechanisms of plant-based foods systematically and comprehensively during growth, maturation, and processing, which contribute to flavor improvement and value enhancement of plant-based foods. By focusing on plant-based foods, the composition and flavor characteristics of key flavor substances based on the structural characteristics of flavor substances in plant-based foods, such as fatty compounds, aromatic compounds, heterocyclic compounds, and terpenes was systematically introduced. Furthermore, the biological flavor formation mechanism and recent advances of plant-based foods from both endogenous and exogenous perspectives at the molecular level were elaborated. Endogenous biological flavor formation primarily involved in the natural generation of characteristic flavor substances in plant-based foods through carbohydrate pathways, protein pathways, fatty acid pathways, and terpene pathways catalyzed by endogenous enzymes. Exogenous biological flavor formation relied on added enzymes or microorganisms to achieve the targeted synthesis of desired flavor compounds or the inhibition of undesirable flavor compounds through bio-catalysis and fermentation techniques. In the future, with the combination of multi-omics technology and interdisciplinary approaches, a deeper understanding of the biosynthetic pathways, regulatory mechanisms, and interactions of flavor substances in plant-based foods will be achieved. This will provide a scientific basis for product improvement and innovation in the food industry, facilitating the development and industrial-scale production of new products.