Although Codonopsis pilosula (C. pilosula) has long been considered as an important herbal medicine, no analytical method of marker compounds for quality assessment is registered in the Korean Pharmacopoeia. We developed a simple and robust analytical method of three marker components lobetyolin (1), lobetyol (2), and tangshenoside I (3) using HPLC-UV method. We also confirmed the three marker components using UPLC-qTOF/MS method. Various extraction conditions were optimized to achieve three marker compounds with faster extraction kinetics and higher recovery. The analytical condition was then validated by determining the linearity, accuracy, precision, limit of detection, limit of quantification, recovery, repeatability, robustness, and stability. By this method, the three markers were successfully quantified in 38 commercial samples along with three related species that are sometimes used as alternatives to C. pilosula. Finally, principal component and hierarchical clustering analyses were conducted to show the practicality of the method developed for the quality evaluation of C. pilosula.