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Background: Insulin resistance (IR) is a common symptom in obese polycystic ovary syndrome (PCOS) patients, as well as in non-obese PCOS patients. Gut microbiota is closely related to IR. However, the relationship between gut microbiota and IR remains unclear in non-obese PCOS patients. Objective: To analyze the composition of the gut microbiota population in non-obese PCOS-IR patients compared to PCOS alone and healthy women. Methods: In the present study, fecal samples from non-obese PCOS patients with and without IR and healthy women were analyzed by 16S rRNA gene sequencing. Moreover, serum hormone levels were detected on the third day of menstruation, and the correlation between gut microbiota and serum hormone was analyzed using R language.Results: We found that the gut microbiota character differed in each group, and the gut microbiota abundance of PCOS-IR group was remarkably reduced.The abundance of Ruminococcaceae_UCG-004 and Acetanaerobacterium in the PCOS-IR group was significantly lower than that of the PCOS-NIR group. Furthermore, the comparison between PCOS-IR and control group revealed that g__Fusobacterium and g__Faecalibaculum were the unique genus of the PCOS-IR group. Moreover, the relationship between gut microbiota, IR, and serum sex hormones was determined. In PCOS with IR group, the relationship between gut microbiota and androgen was more significant. In PCOS without IR group, the relationship between gut microbiota and androgen was no significant. Its mechanism may be related to the different abundance in enzymes (futalosine hydrolase, arogenate dehydrogenase (NADP(+), and L-lysine 6-transaminase) and metabolic pathways (isoquinoline alkaloid biosynthesis, styrene degradation, and atrazine degradation), but it needs to be further explored in subsequent experiments. Conclusion: The gut microbiota composition of non-obese PCOS patients with insulin resistance is different from that of PCOS alone and healthy women. The difference is correlated with the clinical characteristics of PCOS, with regards to insulin resistance and sex hormone. The abnormality of gut microbiota may lead to the occurrence and development of PCOS-IR. All in all, this study not only provided supplements for the existing studies, but also revealed the potential pathogenic bacteria genus, thus providing a new idea for the treatment of PCOS with IR.