Gardenia fruits, commonly used in traditional Chinese medicine, historically treated jaundice and hepatitis. Despite the pharmacopeial identification of the source plant as Gardenia jasminoides Ellis (MG), market occurrences of adulteration with G. jasminoides var. Radicans Makino (WG) have been noted. This study aims to compare and analyze the therapeutic potential of the main components of MG and WG on jaundice and hepatitis using network pharmacology methods, exploring WG as an alternative or supplementary resource to MG. Network pharmacology and molecular docking methods compared the main components of WG and MG, as well as their mechanisms of action in treating jaundice, hepatitis, and related disorders. Additionally, cell experiments using RAW 264.7 cells assessed the effects of Geniposide, Genipin, Crocin, Crocin II, and Crocetin on Cell Counting Kit-8 (CCK-8), nitric oxide (NO) production, and the secretion levels of TNF-α, IL-6, and IL-1β, measured through enzyme-linked immunosorbent assay (ELISA). WG and MG exhibited common targets in treating jaundice, hepatitis, and related disorders, with GO and KEGG analysis showing high similarity, all pointing to inflammation-related pathways. Toxicity prediction and molecular docking identified five shared compounds (Crocin, Crocin II, Geniposide, Genipin, and Crocetin) among WG and MG, demonstrating significant pro-proliferative effects on LPS-induced RAW 264.7 cells and inhibitory effects on inflammatory factors NO, TNF-α, IL-6, and IL-1β. Through network pharmacology comparative analysis, we found that WG and MG have a similar chemical basis for treating jaundice and hepatitis, with the analysis of their mechanisms of action pointing to inflammation-related pathways. Shared components such as Geniposide, Genipin, Crocin, Crocin II, and Crocetin exhibited significant anti-inflammatory activity, effectively countering the inflammatory effects induced in LPS-treated RAW 264.7 cells. Despite the limited acceptance of WG in medical practice, this study provides new perspectives and clues for its development.