Processing technologies such as thermal treatment, fermentation, or wine-steaming, profoundly influence the chemical composition and functional properties of plant materials, yet its role in generating potentially functional compounds remains underexplored. Herein, feature-based molecular networking (FBMN) was employed to investigate processing-driven molecular transformations in Ligustri Lucidi Fructus and its wine-steamed product. In total, 159 compounds, including 93 iridoids and 25 phenylethanoids, were systematically annotated, thereby expanding the known chemical diversity of the processed product. Multivariate statistical analysis identified 48 differential metabolites associated with processing, revealing extensive chemical transformations, particularly among iridoid-related constituents. Molecular docking analyses suggested that processing-enriched metabolites with distinct scaffold types or cinnamoyl-containing moieties exhibited favorable interactions with ESR1, a target associated with osteoporosis-related pathways. To provide preliminary functional validation, representative processing-enriched iridoids were evaluated using in vitro osteoclastogenesis assays, where loganetin and oleoside 11-methyl ester inhibited osteoclast differentiation. Overall, integrating FBMN-assisted metabolomics with processing chemistry and cell-based validation provides a strategy for characterizing processing-induced metabolite diversification and exploring their potential functional relevance in plant materials.