Cinnamoylquinic acid derivatives, namely, 3,4,5-tri-caffeoylquinic acid (TCQA) and its structurally modified analogue, 3,4,5-tri-feruloylquinic acid (TFQA), have demonstrated promising neuroprotective and pro-neurogenic activities. However, it remains unclear how the substitution of caffeoyl groups with feruloyl groups influences their molecular activity. Therefore, we performed an integrated multi-omics analysis, combining post hoc transcriptomic profiling of TCQA- and TFQA-treated neural stem cells (NSCs) isolated from 6 to 8-week-old adult male ICR mouse brains with targeted metabolomic analysis in SH-SY5Y neuroblastoma cells. We applied an interaction-only nested linear model, which revealed gene sets uniquely responsive to TFQA compared with TCQA. TFQA elicited broader pathway enrichment involving cell signaling, immune modulation, and metabolic regulation, whereas TCQA produced narrower transcriptional shifts. Nested comparative modeling identified 709 genes differentially regulated between TFQA and TCQA, with TFQA uniquely enriching pathways such as glutamatergic synapse, long-term potentiation, TRP channel regulation, and apelin signaling. Downregulation of cell cycle–related pathways and cytokine secretion suggested that TFQA promotes neuronal differentiation while reducing inflammatory activity. Metabolomic profiling further demonstrated TFQA-specific alterations in central energy metabolism, redox balance, amino acid utilization, and neurotransmitter-related metabolites. TCQA showed carbohydrate metabolism and glycan turnover. Integrated pathway analysis and gene–metabolite network modeling revealed coordinated TFQA-associated molecular reprogramming, with metabolites such as ATP, GTP, glutamate, GABA, and L -arginine emerging as central hubs linking transcriptomic and metabolic responses. Collectively, this study provides a multi-layered, systems-level comparison of TCQA and TFQA across a cross-species, cross–cell-type framework, revealing both conserved and divergent molecular responses and offering insights into the structure–activity principles shaped by feruloyl substitution.