Background <p>Polycystic ovary syndrome (PCOS) is widely acknowledged as the prevailing reproductive endocrine disorder accompanied by numerous metabolic dysfunctions. However, there has been a lack of systematic examination regarding the amino acids profile in PCOS. There is a dearth of evidence in regard to the examination of connections between amino acid metabolites found in follicular fluid (FF) and the quality of embryos during in vitro fertilization (IVF).</p> Objective <p>Our objective was to assess amino acid signatures associated with PCOS, as well as identify potential amino acid markers for evaluating embryo quality in PCOS.</p> Methods <p>The cohort study consisted of 143 women who were undergoing lVF/ICSl. Among these, 79 patients who had been diagnosed with PCOS, while the remaining 64 patients did not have PCOS. The concentrations of 30 amino acids present in FF were accurately determined through the use of high-performance liquid chromatography-tandem mass spectrometry. We use the spearman correlation was used to calculate correlations. Odds ratio (ORs) and 95% CIs between differential metabolites and embryo mass were estimated by the logistic regression.</p> Results <p>The concentrations of glutamine (<i>p</i> = 0.025), taurine (<i>p</i> = 0.017), phenylalanine (<i>p</i> = 0.006), arginine (<i>p</i> = 0.002), histidine (<i>p</i> = 0.001), serine (<i>p</i> = 0.001), Tryptophan (<i>p</i> = 0.037), citrulline (<i>p</i> = 0.05), lysine (<i>p</i> = 0.012), sarcosine (<i>p</i> = 0.028) and 1-Methylhistidine (<i>p</i> = 0.006) in the PCOS group were significantly lower than those in the control group. Both PCOS and control groups showed distinct amino acid profiles between quality subgroups: in PCOS, taurine, aspartic acid, and threonine were higher in the top-quality subgroup, while in controls, alanine, glutamic acid, tyrosine, tryptophan, glycine, ornithine, threonine, and methionine were lower in the poor-quality subgroup. Lower amino acid concentrations were associated with a lower probability of high-quality embryos from IVF. We also identified 11 and 3 amino acids that related to embryo quality in the control and PCOS groups respectively.</p> Conclusion <p>Our research has the potential to provide valuable insights regarding the involvement of amino acid abnormalities in follicular fluid in the pathophysiology of PCOS. The findings indicated the possibility of variations in amino acid composition, and consequently variations in embryo quality, among normal and PCOS women. Additional research is required in order to substantiate these findings and directly assess the effects on pregnancy and live birth outcomes.</p>