Background: Using Huanglian Jiedu decoction (HJD) as a model, this study systematically compares the traditionally prepared combined decoction with mixtures of separately decocted components, focusing on differences in chemical composition, material properties, and transcriptomic responses. Methods: To maintain consistency, both the combined HJD decoction and the single-herb mixture were prepared using a standardized method, and their chemical profiles were analyzed by HPLC and UPLC-MS/MS to identify constituent differences. Physical properties were examined through key parameter measurements and phase behavior analysis, and the integration of chemical and physical data identified the components driving the observed material changes. Transcriptome sequencing compared the two decoction types, highlighting differentially expressed genes and the major regulatory pathways involved. Results: HPLC analysis showed a clear redistribution of components between the two decoction methods, with the combined decoction containing higher levels of alkaloids such as coptisine chloride, epiberberine, palmatine chloride, jatrorrhizine hydrochloride, and phellodendrine chloride, while the single decoction mixture had higher levels of berberine hydrochloride and baicalin. In the combined decoction, the berberine hydrochloride content was 37.04 mg/g, and the baicalin content was 15.57 mg/g; in the single decoction, the berberine hydrochloride content was 41.15 mg/g; in the combined decoction, the baicalin content was 40.07 mg/g. UPLC-MS/MS analysis confirmed clear differences between the two decoctions, mainly in flavonoid and alkaloid compositions. The combined decoction contains 110 flavonoid compounds and 67 alkaloid compounds, while the single decoction contains 100 flavonoid compounds and 80 alkaloid compounds. Physical measurements showed that the combined decoction had higher total dissolved solids, conductivity, and salinity, while the single decoction had higher resistivity. The combined decoction had a TDS of 2480 mg/L, σ of 4.95 ms/cm, S of 0.26%, and ρ of 202 Ω·cm; the single decoction had a TDS of 1190 mg/L, σ of 2.37 ms/cm, S of 0.12%, and ρ of 419 Ω·cm. Phase separation analysis indicated that the combined decoction formed a stable nanoscale phase structure, whereas the single decoction remained unstable. Transcriptome sequencing at various concentrations revealed marked differences in gene expression between the two preparations, reflecting their distinct biological activities. Conclusions: Analysis showed clear differences in chemical composition, physical properties, and gene expression in the combined decoction. Taking Huanglian Jiedu decoction as a representative example, we systematically compared the specific differences between combined and single decoction methods, providing a reference basis for subsequent pharmacodynamic evaluation and clinical application.