The genus Cymbidium, with its intricate floral elements, pronounced endemicity, and patchy distribution, evolves a rich diversity of morphological forms and a wide variety of species while causing an indistinctness in the classification of its species. To elucidate the phylogenetic relationships among Cymbidium species and enhance their taxonomic classification by DNA barcoding, this study conducted amplification and sequence results of nuclear (ITS) and chloroplast genes (matK, rbcL, trnL-F, psbA-trnH) with phenotypic genetic diversity analysis, genetic distance analysis, and phylogenetic analysis from 48 samples of Cymbidium species. The comparison of genetic distance variations showed that psbA-trnH, ITS + psbA-trnH, and ITS + matK + psbA-trnH exhibit minimal overlap and significant genetic variation within Cymbidium species. The phylogenetic analysis indicated that the combination, ITS + matK + psbA-trnH, has the highest identification rate. Notably, both the phylogenetic analysis and the genetic diversity analysis of phenotypic traits consistently indicated a clear divergence between epiphytic and terrestrial orchids, with epiphytic orchids forming a distinct clade. This provides reference evidence for studying the ecological adaptations and evolutionary differences between epiphytic and terrestrial orchids, as well as a scientific basis for the classification and identification, germplasm conservation, resource utilization, and phylogenetic evolution of orchids.