Objective This study focused on the root of Polygala tenuifolia by distinguishing the root, root bark (after removal of the heartwood), and heartwood from roots of different diameters, a high-performance liquid chromatography (HPLC) fingerprint was established. Combined with chemical pattern recognition and multi-index component content determination methods, the quality differences were systematically evaluated to provide a scientific basis for the traditional “Quality Assessment Based on Morphological Characteristics” theory, specifically the principle that “thicker bark indicates better quality”. Methods P. tenuifolia samples were collected from Yulin, Shaanxi, and grouped according to root diameter (2, 3, 4, 5, 6, 7 mm). The root, root bark, and heartwood samples were prepared separately. HPLC was used to establish fingerprints, calibrate common peaks, and identify the main components. The contents of seven indicator components, such as tenuifolin, were determined. Principal component analysis (PCA) and orthogonal partial least-squares discriminant analysis (OPLS-DA) were performed using SIMCA 14.0 software, and cluster heat-map analysis was conducted on the Metware Cloud platform. Results HPLC fingerprints of 18 batches of samples were established, with 23 common peaks calibrated and seven of them identified. Similarity ranged from 0.748 to 0.943. PCA and OPLS-DA clearly distinguished three sample types (root, root bark, heartwood) and screened nine differential components, including 3,6′-disinapoyl sucrose and onjisaponin B. Overall, the content of active components followed the order: root bark > root > heartwood. 3,6′-disinapoyl sucrose showed significant differences between root bark and heartwood, while polygalaxanthone III varied markedly between root and root bark. The total content of indicator components increased with root diameter and bark thickness, but the individual content fluctuated irregularly with diameter, which may be related to the ratio of bark to heartwood. Conclusion The established HPLC fingerprint, combined with chemical pattern recognition and multi-index content determination, is stable and reliable. It can be used to systematically evaluate the quality differences of P. tenuifolia roots, root barks, and heartwoods of different diameters, providing a scientific reference for quality control and rational utilization of P. tenuifolia medicinal materials.

Polygala tenuifolia Willd.  /  root  /  root bark  /  heartwood  /  fingerprint  /  chemical pattern recognition  /  sibiricose A5  /  sibiricose A6  /  polygalaxanthone III  /  3,6′-disinapoyl sucrose  /  tenuifoliside A  /  tenuifolin  /  onjisaponin B