Dietary puerarin at 200 mg/kg significantly improved egg quality, laying rates, and feed efficiency in aging hens while restoring hormone balance and reducing ovarian oxidative stress. The isoflavone enhanced hepatic vitellogenin synthesis through metabolic pathway activation and reversed gut dysbiosis by increasing beneficial Lactobacillus and Bacteroides populations. Multi-omics analysis revealed puerarin targets PPAR signaling pathways linking gut microbiome changes to improved liver metabolism and ovarian function. This research provides compelling evidence for the gut-liver-reproductive axis concept, where microbiome health directly influences reproductive longevity through metabolic intermediates. The findings have broader implications for understanding how phytoestrogens might support reproductive health during aging in mammals. While the hen model offers valuable insights into reproductive aging mechanisms, translating these specific dosages and pathways to human applications requires caution. The study's strength lies in its comprehensive multi-omics approach linking microbiome, metabolism, and reproductive function. For women experiencing age-related reproductive decline, this suggests dietary isoflavones might offer support, though human clinical trials would be essential to confirm therapeutic potential and optimal dosing strategies.