The chlorogenic acids are the major bioactive constituents of the whole plant of Ainsliaea fragrans Champ. (Xingxiang Tuerfeng). These compounds are usually present as isomeric forms in Xingxiang Tuerfeng. Therefore, an efficient approach should be developed for the rapid discovery and identification of chlorogenic acids isomers through the fragmentation pathway and rules. In this study, the collision induced dissociation tandem mass spectrometry (CID-MS/MS) fragmentation routes of chlorogenic acids were systematically investigated by UHPLC-QTOF-MS/MS in the negative ion mode using eight chlorogenic acids standards. As a result, diagnostic product ions for rapid discovery and classification of chlorogenic acids isomers were determined according to their MS/MS fragmentation patterns and intensity analysis. Based on these findings, a novel two-step data mining strategy was established. The first key step was to screen different kinds of substitution and the skeleton of the quinic acid using the characteristic product ions and neutral losses. The second key step was to screen and classify different types of chlorogenic acids using their diagnostic product ions. It was apply to the rapid investigation, classification, and identification of chlorogenic acids. And the same carbon skeletons from a complex extract of Ainsliaea fragrans Champ. were effectively identified. 88 constituents, including 14 chlorogenic acids types, were rapidly discovered and identified, and in particular, 12 types of chlorogenic acids, including p-CoQC, FQA, BQC, CQA-Glu, CFQA, p-Co-CQC, di-p-CoQC, BCQA, di-CQA-Glu, PCQA, tri-QCA, and P-di-CQA, were first discovered in Ainsliaea fragrans Champ. In conclusion, UHPLC-QTOF-MS/MS method together with a systematic two-step data mining strategy was established as a feasible, effective, and rational technique for analyzing chlorogenic acids. Additionally, this study laid a foundation for the study of the active substances and quality control of Ainsliaea fragrans Champ.