A simple gradient high-performance liquid chromatography with diode array detection (HPLC-DAD) method was used to simultaneously to analyze characteristics of six indicator compounds in the traditional Chinese medicine (TCM) formulation Wen-Qing-Yin (WQY). Separate optimization was performed using a Cosmosil C18 column gradient method with 0.1% formic acid in both mobile phases of aqueous and acetonitrile (ACN), at a flow rate, detection wavelength, and sample volume of 1.8 mL/min, 268 nm, and 10 μL, respectively. The linear regression of six active compounds berberine (BER), baicalin (BAI), ferulic acid (FER), geniposide (GEN), hydorxymethoxylfurfural (HMF), and paeoniflorin (PAE) was produced at the concentration range of 10–2000 μg/mL. The method validation revealed an acceptable precision (intra- and inter-day precision < 3.39% and 4.11%, respectively) and recovery (85.60–110.45% and 86.58–110.90%), a recovery range of 86.61–109.42%, and sensitivity (limit of detection [LOD] and limit of quantification [LOQ] values were in the range of 0.03–3.13, and 0.08–9.38 μg/mL, respectively) while the calibration curves were linear with a correlation coefficient (R2) ranging from 0.9966 to 0.9989. The qualitative and quantitative analyses were performed by direct comparison of the peaks of the WCY extract to retention times of reference standards. Additionally, principal component analysis (PCA) successfully discriminated four purchased commercial samples of all six indicator constituents, and the present results indicate their comprehensive potential usefulness for qualitative and quantitative analyses of the WQY decoction and its commercial products.