Bioactive Ingredient Profiling of Dendrobium officinale: Plant-Part-Specific Distribution of Key Metabolites and Their Multi-Disease Therapeutic Potential

Background/Objectives: Dendrobium officinale is a valuable medicinal orchid. However, the metabolic profiles of its leaves and flowers remain poorly characterized. This highlights the need for comprehensive analysis of stems, leaves, and flowers to reveal plant-part-specific bioactive compounds and expand whole-plant utilization. Methods: An integrative metabolomic approach based on UHPLC–MS/MS was employed to systematically characterize secondary metabolite profiles in different parts of D. officinale, including stems (DOS), leaves (DOL), and flowers (DOF). Results: A total of 761 metabolites, predominantly flavonoids (30.6%), alkaloids (20.2%), phenolic acids (12.2%), and terpenoids (9.3%), were identified. The most abundant metabolites were detected in DOF (634), followed by DOL (598) and DOS (586). Total flavonoid and alkaloid contents were the highest in DOF, reaching 0.86 and 0.62 mg·g−1 DW, respectively. Screening identified 74 key active ingredients (KAI) and 83 active pharmaceutical ingredients (API) and demonstrated potential efficacy against six major human diseases. Among these, gardenoside and phloroglucinol were uniquely present in leaves, whereas 12 KAIs and 16 APIs were specific to DOF. Quercetin, a compound associated with more than 90 disease-related entries, was exclusively detected in DOF. Multivariate analyses revealed clear separation among the three plant parts. Furthermore, 15 metabolites with VIP > 1, including pinobanksin and naringenin, exhibited distinct plant-part-specific accumulation patterns. Additionally, potential plant-part-specific biomarkers were identified. Conclusions: This study presents a comprehensive plant-part-specific metabolomic profile of D. officinale, revealing that its flowers and leaves are particularly enriched in bioactive flavonoids and alkaloids. The findings reveal the remarkable metabolic diversity and functional potential of D. officinale, providing essential chemical insights that support the whole plant’s broader medicinal and biotechnological applications.