Dendrobium officinale is a precious traditional Chinese herbal medicine in China. It has plenty flowers and blooms from March to June. However, a large amount of D. officinale flower resources are wasted, due to the lack understanding of its bioactive component composition. Therefore, a comprehensive analysis of bioactive component composition and their metabolism pathway were performed by Biotechnology Breeding Research Group using transcriptome and metabolome analysis to identified the bioactive compounds and screened the key metabolic genes. Our data showed that the D. officinale flowers are abundant in flavonoids, carotenoids and linolenic acid, which are helpful to human health. Interestingly, the main water-soluble polysaccharide in D. officinale flowers is mannan, which gradually accumulates during the flower development. We analyzed the transcriptional level of the mannan polysaccharide biosynthesis genes, including nucleotide sugar biosynthesis genes, nucleotide sugar transporter genes and cellulose synthase-like A (CSLA) genes. These genes were strongly correlated with the accumulation of mannan. The key genes involved in the biosynthesis of bioactive compounds were identified and the expression patterns of these genes were consistent with the accumulation of bioactive compounds. In addition, the content of phytohormone auxin decreased during flower development, and its synthesis pathway genes also changed consistent with it. The abscisic acid increased gradually during flower development, and the expression level of key gene NCED for ABA synthesis was the highest in opened flowers. These results indicated that phytohormone auxin and ABA were involved in flower development in D. officinale. These work not only provide important scientific basis for the development and utilization of D. officinale flower products, but also provide important gene resources for the in-depth study of the metabolism of bioactive compounds, and provide ideas for the molecular mechanism of orchid flower development.