Lonicera japonica Thunb. is a well-known traditional herbal medicine in most East Asian countries. In China, the flower bud and stem of this plant are used for various clinical therapies, while the leaf is not officially recognized as an active part. Due to the similarities in their chemical constituents but great differences in their commercial values, the flower bud has been found to be adulterated with leaf and/or stem during the production of formulations by some drug manufactures. In order to identify adulteration in products and enable quality control, it is necessary to chemically discriminate these three parts of L. japonica. In the current study, an HPLC-ESI-MS(n) method was developed and validated for the quantitative analysis of 18 bioactive compounds: 7 organic acids, 6 iridoids, and 5 flavonoids, in batches of flower bud, stem, and leaf samples. Subsequently, chemometric analyses, such as one-way analysis of variance, principal component analysis, and hierarchical clustering analysis, were performed based on the quantitative data. The results indicated that there were remarkable differences in the distribution of the investigated compounds among the three parts of L. japonica, and that they could be straightforwardly and reliably distinguished according to their chemical profiles. Twelve compounds were selected as potential differential metabolites, which would be useful for quality control of L. japonica. As the content of caffeic acid was low in the flower bud but much higher in the stem and leaf, it could be used as a chemical marker to identify adulteration.