Background: Bletilla striata (Thunb.) Rchb.f., a perennial medicinal plant in the genus Bletilla of the Orchidaceae family, is renowned for its hemostatic, anti-inflammatory, and tissue-regenerative properties. Despite the established importance of polysaccharides as key bioactive components in B. striata, the genes and molecular mechanisms underlying their synthesis remain largely unexplored. Methods: This study conducted transcriptomic analysis on the roots, tubers, and leaves of B. striata, and identified gene expression profiles and candidate genes for polysaccharide synthesis in different organs. Results: The results indicated that there were 7699 differentially expressed genes (DEGs) in Tuber vs. Leaf, 7695 DEGs in Luber vs. Root, and 6151 DEGs in Tuber vs. Root. There were significant differences in polysaccharide metabolism pathways (photosynthesis, starch, and sucrose metabolism) in different organs of B. striata. The overall enrichment levels were ranked as tubers > leaves > roots. It is worth noting that enzyme genes involved in polysaccharide synthesis exhibit significant organ specificity, with HK genes expression significantly higher in roots than in tubers and leaves, PMM, GMPP, pgm, and UGP2 genes highly expressed in tubers, while scrK, manA, and GPI genes have similar expression levels in the three organs. Conclusions: These findings identify key enzyme genes involved in the synthesis of polysaccharides in B. striata, providing a theoretical framework for enhancing its medicinal value through genetic improvement.