Electrolytic hydrogen water (EHW) plays a critical role in modulating cellular metabolism; yet, the underlying molecular mechanisms remain unclear. This study utilized next-generation sequencing (NGS) to assess mRNA and miRNA expression in EHW treated Caco 2 cells. Bioinformatics analysis identified differentially expressed genes (DEGs) and pathways influenced by EHW and highlighted its involvement in the oxidative stress response and tight junction formation. Protein-protein interaction (PPI) network analysis of the DEGs identified first neighbor genes, supporting the role of EHW in suppressing oxidative stress related genes while also enhancing the expression of the TCEB2 CUL5 COMMD8 (ECS complex) genes, both of which converged on the HIF1 signaling pathway. We also constructed an mRNA and miRNA competing endogenous RNA (ceRNA) network, which revealed four hub genes, two non-coding RNAs (miR-429 and miR-200c-3p) and two protein-coding RNAs (CUL5 and GOLGA7). These genes co-target the transcription factor KLF4 in Caco 2 cells, forming a TF miRNA gene network (TMGN). EHW treatment significantly decreased the levels of miR 429 and miR 200c 3p and stabilized CUL5 and GOLGA7 transcripts post-transcriptionally as compared to ACW. Concurrently, reduced miRNA expression weakened their pretranscriptional competition with mRNAs for KLF4 binding, further enhancing CUL5 and GOLGA7 expression. Phenotypic assays confirmed that continuous EHW treatment promotes Caco 2 cell differentiation. This study underscores the regulatory role of EHW in intestinal cells via feed-forward loops (FFLs), offering novel insights into the molecular mechanisms and functions of EHW.