Polygonum multiflorum Thunb. is a perennial plant that belongs to Polygonaceae. Root tissues are the main plant parts used as medicinal herbs in Korean oriental medicine. The P. multiflorum tuber is well known for its medicinal properties in Korean oriental medicine, and it contains a number of useful substances (secondary metabolites of emodin, 2,3,5,4′-tetrahydroxystilbene-2-O-β-d-glucoside (TSG), etc.) that are increasing in demand, as several studies show that they have beneficial effects on the human body. In this study, the production volumes and useful material content differences between cultured P. multiflorum seedlings (culture seedlings: CSs), which had been grown using a tissue culture technique under optimized conditions, and existing varieties in circulation (seed seedlings: SSs) were determined using a long-term field test. The growth characteristics of the underground parts were investigated by harvesting the tuberous roots (medicinal parts) after 1 year, and the results showed that the fresh and dry weights of the CS tubers were higher than those of the SS tubers. However, the SS rootlets had higher fresh and dry weights than the CS rootlets. A liquid chromatography-mass spectrometry component analysis of the P. multiflorum tubers and a Fourier transform near-infrared spectrophotometer analysis of the roots were undertaken. The results showed that the levels of TSG, which is a medicinal substance produced by P. multiflorum, were higher in the CSs than in the SSs, but the differences were not significant. The CS results from this study will inform future studies on the mass production of P. multiflorum in the field because the medicinal area was greater in CSs than in SSs.