The flavonoids in Tetrastigma hemsleyanum Diels et Gilg (T. hemsleyanum) have high medicinal value. However, because of slow growth and harsh ecological environments, T. hemsleyanum is currently an endangered species. In light of this, we present a detailed hairy root induction procedure as a promising alternative to true roots with medicinal value. The percentage of explants induced by Agrobacterium rhizogenes (A. rhizogenes) to produce hairy roots out of the total number of explants infected (induction rate 1) was 95.83 ± 7.22%, and the proportion of hairy roots that contained Rol B fragments among all the hairy roots with or without Rol B fragments (positive rate) was 96.57 ± 1.72%. The transformation was further confirmed by the expression of the GUS protein. A high-productive hairy root line was screened for the comparative profiling of six flavonoids with true roots using high-performance liquid chromatography (HPLC). The contents of (+)-catechin, (−)-epicatechin, neochlorogenic acid, luteolin-6-C-glucoside, and orientin were 692.63 ± 127.24, 163.34 ± 31.86, 45.95 ± 3.46, 209.68 ± 6.03, and 56.82 ± 4.75 μg/g dry weight (DW) of 30-day-old hairy roots, respectively, which were higher than those of 3-year-old true roots. Hairy roots have stronger antioxidant activity than true roots. Overall, the hairy roots of T. hemsleyanum could serve as promising alternative sources for the production of flavonoids with medicinal uses.