Based on chromatographic fingerprinting combined with quantitative analysis on characteristic chemical constituents as well as hierarchical cluster analysis, an easy and sensitive approach utilizing high performance liquid chromatography (HPLC) was developed for the identification and quality evaluation of Rutongshu oral liquid (ROL). What is more, nontargeted metabolomic analysis was conducted to gain a global view in terms of its chemical profile. In this study, 16 peaks from different batches (S1–S10) of ROL samples produced by Taihe Hospital of Chinese Medicine were selected as common peaks for the evaluation of their similarity whose values of all tested 10 batches exceeded 0.90 when compared with the control fingerprints. Meanwhile, simultaneous quantification of five markers in the oral solution, including albiflorin, paeoniflorin, chlorogenic acid, quercetin and ferulic acid was performed, and standard curves established for respective reference substances showed good regression in the linear range (r2 > 0.999) with recoveries in the range of 98.96–102.35%. The ultra-high performance liquid chromatography (UHPLC) combined with Orbitrap Exploris 120 mass spectrometer resulted in 88 identified compounds. The results of validation showed that the established method was reproducible, precise and stable. This study offers an effective, dependable and useful approach for the systematic evaluation of the hospital formulation ROL.