[Objective] The research aimed to study HPLC fingerprint of isoflavonoids content in Heshui Pueraria thomsonii Benth. root and provide theoretical basis for reasonable development and utilization of this resource. [Method] Puerarin was served as the standard substance,the contents of total isoflavonoids and puerarin,the constituent of the isoflavonoids in fibrous and in the head,middle,tail,epidermis,subcutaneous tissue of tuber root were studied by HPLC. [Result] The contents of total isoflavonoids and puerarin in epidermis of Heshui Pueraria thomsonii Benth. root were both greatly higher than that in subcutaneous tissue. The contents of total isoflavonoids and puerarin in tail tuber root were lower than that in head and middle parts. The content of total isoflavonoids in fibrous root was higher than that in the tuber root. But the content ratio of the puerarin in isoflavonoids was much lower than that in the tuber root. And there was an unknown isoflavonoid whose content was close to the puerarin. [Conclusion] The contents of total isoflavonoids and puerarin as well as the constituent of the isoflavonoids in different parts of Heshui Pueraria thomsonii Benth. root were different. [Objective] The research aimed to study HPLC fingerprint of isoflavonoids content in Heshui Pueraria thomsonii Benth. Root and provide theoretical basis for reasonable development and utilization of this resource. [Method] Puerarin was served as the standard substance, the contents of total isoflavonoids and puerarin, the constituent of the isoflavonoids in fibrous and in the head, middle, tail, epidermis, subcutaneous tissue of tuber root were studied by HPLC. [Result] The contents of total isoflavonoids and puerarin in epidermis of Heshui Pueraria thomsonii Benth. root were both greatly higher than that in subcutaneous tissue. The contents of total isoflavonoids and puerarin in tail tuber root were lower than that in head and middle parts. The content of total isoflavonoids in fibrous root was higher than that in the the tuber root. But the content ratio of the puerarin in isoflavonoids was much lower than that in tuber root. And there was an unknown isoflavonoid whose content was close to the puerarin. [Conclusion] The contents of total isoflavonoids and puerarin as well as the constituent of the isoflavonoids in different parts of Heshui Pueraria thomsonii Benth. root were different.