Puerariae Lobatae Radix (PLR), a well-known herbal medicine, is the root of Pueraria lobata that has been employed for the treatment and prevention of cardiovascular and cerebrovascular diseases. The purpose of this study was to compare the associated-extraction efficiency of 8 various cyclodextrins on five isoflavonoids, including puerarin, daidzein, daidzin, genistein and genistin, which were the major chemical components with low water solubility in Puerariae Lobatae Radix. Eight various cyclodextrins were applied, including α-cyclodextrin (α-CD), β-cyclodextrin (β-CD), γ-cyclodextrin (γ-CD), hydroxypropyl-β-cyclodextrin (HP-β-CD), hydroxypropyl-γ-cyclodextrin (HP-γ-CD), methyl-β-cyclodextrin (Me-β-CD), carboxymethyl-β-cyclodextrin (CM-β-CD), and sulfobutyl ether β-cyclodextrin (SBE-β-CD). High performance liquid chromatography (HPLC) was established to analyze five flavonoids in various CD extracts and traditional aqueous extracts. Associated-extraction efficiency of various CDs followed the ranking: SBE-β-CD > HP-β-CD > Me-β-CD > CM-β-CD > HP-γ-CD >γ-CD >β-CD >α-CD. Obviously, SBE-β-CD presented the highest associated-extraction capability, and it was applied to extract the five isoflavonoids from three products of PLR, including raw product, stir-frying product, and simmering product with wheat bran. The results showed that SBE-β-CD could improve the extraction capability of isoflavonoids both in raw product and processed products of PLR. In conclusion, CDs, especially SBE-β-CD, has a promising application for associated extraction of isoflavonoids in PLR.