Premature ovarian insufficiency (POI) has become one of the greatest health threats to the reproduction of women during their fertile age. Lycium barbarum polysaccharides (LBPs) are known for anti-aging and reproductive protective functions. Here, we investigated the protective effect of LBP on POI mice and revealed its possible mechanism by a combination of 16S rRNA sequencing and metabolomics analysis. In the current study, female C57BL/6J mice treated with D-galactose were used as a model to investigate the reversal effect of LBP on the degenerative ovarian function. The ameliorative effect of LBP on POI was evaluated from the estrous cycle, ovarian reserve, serum sex hormone levels, and fertility testing. Additionally, 16S rRNA gene sequencing and untargeted metabolomics were integrated to analyze the effects of LBP on the gut microbiota and fecal metabolic profile in the POI mice. The results showed that LBP administration significantly increased the total number of follicles and the number of follicles at different developmental stages in the POI mice. In addition, LBP was effective in reducing the serum levels of follicle-stimulating hormone (FSH) and luteinizing hormone (LH), regularizing the disordered estrous cycle, and increasing the number of offspring of the POI mice. The results from 16S rRNA sequencing showed that LBP had beneficial effects on the composition and structure of the gut microbiota in the POI mice. In a metabolomics study, a total of 23 metabolites were finally identified as potential biomarkers of POI, and multiple pathways were regulated after the treatment of LBP, especially the arginine biosynthesis, glycerophospholipid metabolism and steroid hormone biosynthesis pathways. Pearson's correlation analysis showed that the regulation effect of LBP on metabolites was closely related to Faecalibaculum, Bilophila and Anaerofustis in the gut microbiota. In summary, the results demonstrated that LBP could improve the ovarian reserve and provides evidence both on the gut microbiota and metabolism, which provide beneficial support for the applications of LBP in female ovarian function degeneration.