The quality of traditional Chinese medicine (TCM) prescriptions (TCMPs) is critical to clinical efficacy; however, evaluating their consistency and identifying sources of variability remain challenging. This study proposes an integrated strategy to assess the quality of 100 widely sold TCMPs. A "one-for-all" chromatographic method was employed to analyze 645 sample batches. This large-scale data collection enabled statistical evaluations, such as hierarchical cluster analysis (HCA) and similarity heatmap, to identify quality inconsistencies. The introduction of a TCM-specific mass spectrometry (MS) database allowed for rapid, automated annotation of chemicals across 100 prescriptions and facilitated the tracing of raw material sources. Results indicate that 19% of prescriptions exhibited chemical inconsistencies, which are associated with high market value, low pricing, and substantial price disparities. The MS database allowed rapid annotation of 761 and 673 compounds in positive and negative modes, respectively, in 100 TCMPs, with 73 prescriptions reported for the first time. The tracing efforts succeeded in identifying >40% of the raw material sources for 51 prescriptions. P93 (Yinianjin (YNJ)) is a case in which the chromatographic profiles from three manufacturers displayed inconsistencies. Analysis using the database traced divergent peaks to Rhei Radix et R hizoma (RRER). Verification with self-prepared samples confirmed that manufacturers utilized three distinct botanical sources. This integrated strategy provides a scalable framework for quality control in TCMPs.