Tetrastigma hemsleyanum is a liana plant with promising medicinal and ornamental values. Its calabash-shaped roots (CRs) are served as a traditional Chinese herb. However, it takes a long growth period to form CRs. In the present study, three types of architectural roots, including fine roots (FRs), bar-shaped roots (BRs) and CRs, were employed as materials, and the characteristics of histo-anatomy and digital RNA-seq transcriptome profiles were analyzed. Among the three types of roots, the vascular bundles in FRs were intact, while some of the vascular bundles degenerated in BRs, and only few traces of vascular bundles existed in CRs. Meanwhile, no obvious cell inclusions were found in the cytoplasm of FRs, while a few inclusions were found in BRs, and abundant inclusions were detected in CRs, which might be the main source of medicinal components in roots. The transcriptome profiles and qRT-PCR validation indicated that seven up-regulated genes encoding xyloglucan glycosyltransferase, ACC oxidase, CYP711A1, SHORT-ROOT transcript factor, galacturonosyltransferas, WAT1 and WRKY, and two down-regulated genes encoded LRR receptor-like serine/threonine-protein kinase and CYP83B1, were probably involved in the formation and development of CRs. Besides, GO terms of intrinsic component of membrane, integral component of membrane, cell periphery, membrane part, plasma membrane, membrane, intrinsic component of plasma membrane, cellular chemical homeostasis, and plasma membrane part were probably related to the formation of CRs. KEGG pathways related to the development of CRs probably included MAPK signaling pathway-plant, plant hormone signal transduction, and circadian rhythm-plant. Our finding suggested a probable mode for the formation of CRs.