Propiconazole (PCZ) and Tianfengsu (TFS) are widely used plant growth regulators in vegetable production for improving crop growth, quality, and flavor. This study investigated the effects of PCZ and TFS, applied individually or in combination, on the growth, development, flavor quality, and nutritional components of choy sum (Brassica rapa) and Arabidopsis thaliana, as well as the underlying molecular mechanisms. The results showed that PCZ inhibited the growth of choy sum and Arabidopsis but enhanced the accumulation of flavor compounds such as soluble sugars, proteins, and vitamin C. In contrast, TFS promoted plant growth and increased the content of nutritional components, including chlorophyll and unsaturated fatty acids. Notably, the combined application of PCZ and TFS significantly improved overall plant quality, achieving the optimal balance of flavor and nutritional value while maintaining high yield. Transcriptomic analysis revealed the molecular mechanisms of PCZ and TFS in differentially regulating the expression of brassinosteroid (BR) signaling and downstream metabolism-related genes. Weighted gene co-expression network analysis (WGCNA) further identified key gene modules and hub genes controlling flavor metabolism in choy sum. This study elucidates the synergistic mechanisms of PCZ and TFS in regulating vegetable growth and quality formation, providing valuable insights for the safe production of high-quality choy sum and the development of novel plant growth regulators or elite varieties.