This study was designed for simultaneous determination of 13 chemical marker compounds, namely, protocatechuic acid, chlorogenic acid, caffeic acid, liquiritin, hesperidin, apigetrin, rosmarinic acid, oxypeucedanin hydrate, byakangelicin, apigenin, glycyrrhizin, nobiletin, and 6-gingerol in Gwakhyangjeonggi-san (GJS: Huoxiang-zhengqi-san in Chinese). A quantitative analytical method was developed based on HPLC-PDA with validation in terms of precision, accuracy, and repeatability, and successfully employed for quality evaluation of GJS samples with the help of chemometric techniques such as principal component analysis (PCA) and hierarchical clustering analysis (HCA). The correlation coefficient for the linear regression was > 0.9994. The intra-day and inter-day precision was < 3.0% of the relative standard deviation (RSD) value, and the recovery was in the range 92.5-107.0%, with RSD values < 4.0%, and the repeatability was < 3.0% of RSD. Variations in the quantity were observed in GJS products from different origins, which were classified by PCA and HCA. The quantitative and chemometric analyses indicate the necessity for consistency in GJS production for the purpose of quality control.