Ophiocordyceps sinensis (O. sinensis), a precious traditional Chinese medicine (TCM), exhibits remarkable hepatoprotective effects. However, chemical differences between wild-collected and cultivated products remain insufficiently characterized in relation to liver fibrosis. We combined untargeted ultra-high-performance liquid chromatography–Orbitrap high-resolution mass spectrometry with targeted liquid chromatography–tandem mass spectrometry to compare wild type (WT) and artificially cultivated (AC) specimens. The two sample groups showed distinct metabolic profiles, and targeted analysis supported differences in selected nucleosides, purine derivatives, pyroglutamic acid, and ergosterol. Adenosine, cordycepin, and ergosterol were more abundant in AC extracts, whereas hypoxanthine, deoxyguanosine, guanosine, and guanine were more abundant in WT extracts. Network pharmacology associated selected source-related metabolites with 158 fibrosis-related candidate targets and prioritized a kinase-centered network involving epidermal growth factor receptor (EGFR), proto-oncogene tyrosine-protein kinase Src (SRC), protein tyrosine kinase 2 (PTK2), HRas proto-oncogene, GTPase (HRAS), phosphatidylinositol 3-kinase/protein kinase B (PI3K-Akt), and mitogen-activated protein kinase (MAPK) signaling. Molecular docking and replicated molecular dynamics simulations indicated structurally plausible interactions for complexes of uridine diphosphate N-acetylglucosamine (UDP-N-acetylglucosamine) with HRAS and AKT serine/threonine kinase 1 (AKT1), and of ergosterol with SRC. These findings reveal source-associated metabolic differences between the analyzed WT and AC samples and provide mechanistic insights into their potentially divergent roles in liver fibrosis regulation, which warrant further experimental validation.