Both qualitative and quantitative analyses combined with activity evaluation were used for the integrated quality control study of Pien-Tze-Huang (PZH), a precious lozenge used for 460 years in China. In qualitative analysis, a high performance LC-quadrupole time-of-flight MS method was developed for the identification of chemical profiling in PZH. 27 compounds were unambiguously identified by comparing with reference substances, and 12 compounds were tentatively deduced based on their MS data and comparing with literatures. Then the in vitro anti-inflammatory activity of 27 compounds were evaluated, and 9 saponins, 11 bile acids, taurine and muscone exhibited significant inhibitory activities on TNF-α production with IC values ranging from 12.34 to 147.24 μM. In quantitative analysis, 21 active compounds, selected as quality control markers, were simultaneously detected in 15 batches of PZH samples by ultra-performance LC-triple quadrupole MS. All the analytes were detected within 15 min. Satisfactory linearity was achieved with wide linear range and fine determination coefficient (r > 0.9990). The respective relative standard deviations of intra- and inter-day precisions, repeatability, stability, and recovery were less than 4.32%, 4.94%, 4.78%, 4.87%, and 4.91%. This study established a high sensitive and efficient method for the integrated quality control of PZH, including qualitative and quantitative analyses combined with pharmacological activity evaluation.