Objective To compare the characteristics of gut microbiota and metabolic functions in patients with polycystic ovary syndrome(PCOS), specifically focusing on the differences between obese and non-obese individuals. Methods Sixteen obese PCOS females(BMI≥28 kg/m²), twelve non-obese PCOS females(BMI 18.5-23.9 kg/m²), and fourteen healthy young females(BMI 18.5-23.9 kg/m²) were selected from June 2020 to June 2022 as the non-obese normal group. Additionally, six healthy but obese females(BMI ≥28 kg/m²) were included as the obese normal group. Blood and non-menstrual fecal samples were collected and analyzed from all participants. Fecal samples were sequenced using 16 S rDNA gene sequencing. Plasma metabolomics analysis was performed using liquid chromatography-tandem mass spectrometry. Results Compared to the non-obese normal group, non-obese PCOS showed significant increases in hirsutism scores, acne scores, LH, LH/FSH, testosterone, E2, and dehydroepiandrosterone(P<0.05). In comparison to the obese normal group, obese PCOS exhibited significantly higher hirsutism scores, LH/FSH, and testosterone, along with significantly lower FSH(P<0.05). Differential abundance analysis identified four genera(Finegoldia, Anaerococcus, Sneathia, and Adlercreutzia) significantly associated with obesity status(P<0.05). Finegoldia, Anaerococcus, Sneathia, and Adlercreutzia showed significantly lower abundance in obese females compared to non-obese females(P<0.05). Stratified analysis based on PCOS status revealed a significant negative correlation between Finegoldia and Anaerococcus with obesity in both PCOS and non-PCOS females. There were suggestive but not significant interactions between PCOS and obesity with Sneathia and Adlercreutzia(PPCOS×Obesity=0.090, 0.057). Anaerococcus exhibited a negative correlation with the ratio of indole-3-acetic acid to tryptophan and valine(r=-0.38,-0.30, P=0.007, 0.041), while Adlercreutzia showed a negative correlation with proline and alanine(r=-0.37,-0.32, P=0.012, 0.034). Conclusion In PCOS females, obesity is associated with changes in gut microbiota and plasma metabolites, including the depletion of bacteria producing butyrate and increased tryptophan degradation metabolism. These findings suggest potential interrelationships among gut microbiota, obesity, and PCOS. [ABSTRACT FROM AUTHOR]