Puerariae Lobatae Radix (PLR) is a commonly used herbal medicine in traditional Chinese medicine, whereas Puerariae Lobatae Caulis (PLC), its aerial part, is frequently utilized as an adulterant due to similar morphological features. Conventional identification methods and pharmacopoeial criteria fail to effectively distinguish these two homologous herbs, creating a demand for a precise identification method. Therefore, a Digital ID method was established for their identification. UPLC-QE-Orbitrap-MS coupled with Progenesis QI software was applied to analyze multi-batch samples of PLR and PLC. Common ion information was extracted, and a differential ion matrix was constructed after eliminating blank ions and cross-shared components. High-intensity characteristic ions were defined as exclusive Digital ID for authenticity identification. The Matching Confidence (MC) values of both herbs matching their own Digital IDs were >85%, while cross-matching MC values were <4%. Unlike subjective macroscopic authentication, compendial TLC and single-marker quantification that fail to discriminate the two materials, and spectroscopic methods incompatible with powdered samples, this digital ID framework enables automated objective authentication via quantitative Matching Confidence without manual spectral comparison. This technique achieves accurate and efficient digital identification of the two herbs, facilitating the quality control of PLR and offering a new strategy for the quality assessment of traditional Chinese medicine (TCM).