STUDY QUESTION: Are there distinct variations in the gut microbiome and metabolism among infertile women diagnosed with diminished ovarian reserve (DOR), and how might the gut microbiome influence ovarian function? SUMMARY ANSWER: In DOR patients, Hoylesella abundance correlated with anti-Müllerian hormone (AMH)/antral follicle count (AFC), and stearic acid was identified as a key differential metabolite that was associated with activated PI3K-Akt signaling. WHAT IS KNOWN ALREADY: Accumulating evidence underscores the presence of a 'gut-ovary axis', highlighting a substantial interplay between the intestinal microbiome and ovarian function. However, the specific microbial and metabolic profiles characterizing infertile individuals with DOR remain largely uncharacterized. STUDY DESIGN, SIZE, DURATION: This study was a cross-sectional observational study. We enrolled participants receiving frozen embryo transfer at the First Affiliated Hospital of Zhengzhou University between 1 October 2024, and 31 December 2025. Each participant was limited to a single frozen embryo transfer within the study. PARTICIPANTS/MATERIALS, SETTING, METHODS: A total of 190 participants were included: 91 with DOR and 99 with normal ovarian reserve (NOR). Clinical information and stool specimens were collected from every subject. Sequencing of 16S rRNA and non-targeted metabolomics were implemented to characterize the gut microbiome and metabolome, respectively. Molecular docking analysis and network pharmacology were then implemented to screen for overlapping genetic targets among DOR-associated targets and key metabolite-targeted proteins. MAIN RESULTS AND THE ROLE OF CHANCE: Relative to NOR controls, the DOR population exhibited significantly lower Gut Microbiota Health Index (P = 2.52 × 10-22) and higher Microbiota Dysbiosis Index (P = 8.31 × 10-10). The genus Hoylesella was significantly depleted in the DOR group (P = 0.018). Spearman analysis demonstrated that Hoylesella proportions were significantly positively correlated with AMH and AFC levels. Metabolomics analysis identified 243 differential metabolites across the study cohorts. Among these, four metabolites were associated with Hoylesella, and stearic acid exhibited high predictive performance (area under the curve = 0.89) for distinguishing DOR. Network pharmacology analysis of stearic acid and DOR identified five core targets: tumor necrosis factor, AKT serine/threonine kinase 1, SRC proto-oncogene, non-receptor tyrosine kinase (SRC), peroxisome proliferator-activated receptor gamma (PPARG), and epidermal growth factor receptor. Kyoto Encyclopedia of Genes and Genomes pathway enrichment indicated that the PI3K-Akt signaling pathway was the most significantly enriched. LARGE SCALE DATA: Raw 16S rRNA sequencing data have been deposited in the NCBI Sequence Read Archive under BioProject accession PRJNA1444490. Untargeted metabolomics data have been deposited in MetaboLights under accession MTBLS14194. LIMITATIONS, REASONS FOR CAUTION: The current investigation represents an initial effort to identify the alterations in intestinal microbes and associated metabolites in women with DOR-related infertility through 16S rRNA sequencing and untargeted metabolomics; however, experimental validation of the underlying mechanisms is still missing. Furthermore, the metabolomics analysis in this study did not further stratify by age. WIDER IMPLICATIONS OF THE FINDINGS: Through immunological dysregulation and inflammatory reactions, aberrant alterations in key intestinal microbes and metabolic products likely participate in the underlying mechanisms of DOR. These results provide direction for further research into the causal connections between important microbial species and metabolites in patients with DOR. FUNDING: This research was supported by grant 32271169 from the National Natural Science Foundation of China and the Henan Province Young and Middle-aged Health Science and Technology Innovation Leading Talent Project (Grant No. LJRC2024009). DISCLOSURES: The authors have no conflicts of interest. TRIAL REGISTRATION NUMBER: N/A.