Background: Lonicera japonica Thunb. (LJ) is a famous traditional Chinese medicinal plant. For great viability and important medical value, LJ was introduced from the geo-authentic areas to nonauthentic production areas. However, the quality changes in LJ after plant production remained unclear. Objective: The objective of the study is to analyze the bioactive compounds, the corresponding gene expressions, and the endogenous plant hormone changes after 3-year introduction. Materials and Methods: In September 2014, LJ cuttings were planted in the two sites. In May 2017, LJ flower buds were randomly harvested and divided into three groups for liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS), quantitative real-time reverse transcription-polymerase chain reaction, and indirect enzyme-linked immunosorbent assay, respectively. Results: The results showed that chlorogenic acid significantly decreased while luteoloside and luteolin significantly increased after plant introduction. Gene expression profiles related to biosynthesis pathways showed differentially expressed patterns although most of them were not significantly different. The down-regulated expression of hydroxycinnamoyl-CoA quinate hydroxycinnamoyl transferase genes resulted in a decrease of chlorogenic acid content while the up-regulated expression of key genes related to synthesizing the universal precursor p-Coumaroyl-CoA and the branched luteoloside biosynthetic pathway led to an increase of luteoloside content. Altered endogenous phytohormone levels, especially jasmonic acid, regulate LJ quality changes. Conclusion: The data demonstrate that irrespective of the decrease of chlorogenic acid, the considerable increase of flavonoids demonstrated the benefit of LJ introduction.