Based on the supramolecular "imprinting template" theory, this study systematically investigated the differences in chemical composition and overall quality characteristics between Lonicerae Japonicae Flos and Lonicerae Flos by integrating ultra-performance liquid chromatography (UPLC), total quantum statistical moment analysis, and spectrum-quantitative modeling. UPLC fingerprints of Lonicerae Japonicae Flos and Lonicerae Flos were established, and the "imprinting templates" component clusters were divided by the matching frequency method. Statistical analysis showed that there were statistical differences in area under curve of total quantum (AUC_T) and variance of chromatographic retention time of total quantum (VCRT_T) between Lonicerae Japonicae Flos and Lonicerae Flos, indicating that they were different in terms of total content and species, while mean chromatographic retention time of total quantum (MCRT_T) was similar, indicating that the two had similar imprinting behavior. The similarity of total quantum statistical moments was used to evaluate the composition differences between batches of Lonicerae Japonicae Flos and Lonicerae Flos, and it was found that the components of Lonicerae Japonicae Flos and Lonicerae Flos had both fluctuation and steady-state properties. Spectrum-quantitative modeling identified A₂ (neochlorogenic acid), A₃ (loganic acid), A₇ (rutin and luteolin), A₄ (chlorogenic acid) and A₁₁ (isochlorogenic acid C) as differential "imprinting templates" component clusters. This study highlights the dual characteristics of stability and batch-wise variability in the quality of Lonicerae Japonicae Flos and Lonicerae Flos, and identifies key differential components clusters, providing a novel strategy for quality control in traditional Chinese medicine.