Tomato (Solanum lycopersicum L.) is a premier global crop prized for its high nutritional value and distinctive flavor. Fruit quality is determined by a diverse array of nutrients, including Vitamin C, carotenoids, soluble sugars, organic acids, free amino acids, and phenolics, alongside a complex profile of volatile aroma compounds. Driven by a consumer shift from yield to quality, the regulatory mechanisms underlying tomato nutrition and flavor have become a focal point of research. However, modern commercial breeding has prioritized yield and resistance, leading to the depletion of flavor-related alleles and a widespread decline in flavor across elite cultivars. This review systematically summarizes the biosynthetic pathways and regulatory networks of major nutrients and volatiles, with a specific emphasis on the metaboliccrosstalk between them. Furthermore, we integrate the characteristics of taste tomatoes and the flavor wheel model to elucidate flavor formation through the synergy of sugar-acid balance, aromatic construction, and metabolic pathways. Finally, we discuss the potential of multi-omics and molecular breeding to achieve the concurrent improvement of nutrition, flavor, and yield, providing a theoretical foundation for high-quality tomato breeding.