Gut dysbiosis impacts the recovery of neurological function after spinal cord injury (SCI). Hyperbaric oxygen (HBO) can alleviate SCI, but its effects on the gut microbiota post-SCI remain unclear. This study aimed to clarify the impact of HBO on SCI-induced gut dysbiosis and to explore the mechanisms of locomotor recovery in HBO-treated SCI mice. After establishing different groups of mouse models, bacterial cultures and Basso Mouse Scale (BMS) scores were performed at various time points post-SCI. Intestinal tissues were collected for intestinal permeability assay, histological analysis, immunofluorescence, and qPCR analysis. Flow cytometry and ELISA were used to detect immune-inflammatory cells and cytokines in intestinal tissue. The composition of gut microbiota in fecal samples from each group was also analyzed. Spinal cord tissues were collected for immunofluorescence and untargeted metabolomics analysis. Spearman correlation analysis was used to correlate differential microbiota with differential metabolites. Our results showed that the expression of tight junction proteins was increased after HBO treatment in SCI mice. Metagenomic analysis of the fecal DNA revealed that HBO altered intestinal bacterial composition. Differential metabolites were mainly enriched in pathways, such as glycerophospholipid metabolism, steroid biosynthesis, and glycolysis/gluconeogenesis. Moreover, differential microbiota showed a strong correlation with differential metabolites related to glycerophospholipids. HBO treatment significantly inhibited immune cells and inflammatory cytokines in the gut after SCI. In addition, HBO treatment significantly increased BMS scores and body weight, and repaired damaged cholinergic neurons. Antibiotic-induced gut dysbiosis impaired the recovery of locomotor function and exacerbated intraspinal pathology. However, these effects could be mitigated by HBO treatment. Overall, HBO treatment may improve neurological recovery through multiple regulatory mechanisms including alleviating gut dysbiosis, reducing intestinal inflammation, and rectifying glycerophospholipid metabolic disorders after SCI. These findings highlight HBO as a promising therapeutic strategy for SCI treatment and support its clinical application. KEY MESSAGES: The intestinal microbiota composition of mice changed after SCI. HBO treatment could preserve intestinal barrier integrity, modulate the composition of intestinal microbiota, rectify glycerophospholipid metabolic disorders, and reduce intestinal immune inflammatory responses. Intestinal microbiota identified as the target for HBO therapeutic in SCI recovery. Alleviating SCI-induced gut dysbiosis may be one of the mechanisms underlying the beneficial effect of HBO on neurological functions.