As a representative medicinal plant in the Orchidaceae, Bletilla striata plays a variety of pharmacological roles in the clinic. However, the emergence of counterfeit species is affecting the basic medicinal materials source identification process, for which Bletilla ochracea and Oreorchis foliosa of the Orchidaceae are two representative species. For this study, 13 representative B. striata samples, three B. ochracea samples and three O. foliosa samples were selected for the systematic determination of polysaccharide yields and monosaccharide composition, and further detection of secondary metabolites by HPLC–MS. The results revealed that there was a significant difference in the yields of polysaccharides between B. striata and B. ochracea (p = 0.006). Although the polysaccharides of both species were composed of glucose and mannose, the molar ratio of the two monosaccharides was different, suggesting that the structures of the polysaccharides were different. The metabolomics results showed that there were no differences in the types of metabolites between B. striata and B. ochracea; however, there were differences in the contents of these metabolites. Although there was no significant difference in the polysaccharide yields of B. striata and O. foliosa (p = 0.074) and the monosaccharide composition was the same (glucose and mannose), many different metabolites were screened out between them: six compounds such as C36H34O11 existed only in B. striata, while substance C39H54O22 was unique to O. foliosa. Therefore, based on the analysis of the polysaccharide content and monosaccharide composition, combined with phase metabolomics research, a preliminary distinction between B. striata, B. ochracea and O. foliosa was achieved.