Abstract Neuropathic pain is a chronic, intractable condition characterized by a complex pathogenesis. Hydrogen-rich water (HRW) has been reported to have possible analgesic properties, but the underlying mechanisms remain unclear. To investigate the effects of HRW, we utilized an L4 spinal nerve ligation (SNL) model in both male and female mice. Pain behaviors were quantitatively assessed using paw withdrawal threshold, paw withdrawal latency, and acetone response tests. Fecal microbiota composition was analyzed through 16S rRNA sequencing, and serum bile acids were assessed by liquid chromatography–mass spectrometry. The expression of bile acid membrane receptor Takeda G-protein-coupled receptor 5 (TGR5) and autophagy markers were evaluated in spinal cord, dorsal root ganglia, and colon through biochemistry experiments. Autophagic structures were examined using transmission electron microscopy. We further validated the roles of TGR5 and autophagy in neuropathic pain through experiments using rapamycin treatment and TGR5 knockout mouse models. The effect of HRW on intestinal barrier function was also tested. We found that HRW effectively ameliorated behavioral deficits associated with SNL-induced neuropathic pain. In addition, HRW facilitated the repair of the damaged gut barrier, restored the disrupted intestinal microbiota, and modulated bile acid metabolism in SNL mice. Interventions with hyodeoxycholic acid and deoxycholic acid produced analgesic effects similar to those of HRW. Takeda G-protein-coupled receptor 5 knockdown reversed the therapeutic effects of HRW and rapamycin. Mechanistically, HRW alleviates neuropathic pain by modulating bile acid metabolites linked to intestinal microbiota and directly or indirectly activating TGR5 in the spinal cord, dorsal root ganglia, and colon, thereby promoting autophagy.