Background: Polycystic ovary syndrome (PCOS) is the most common reproductive endocrine disease in women of childbearing age, and insulin resistance is an important etiological mechanism in PCOS. This study revealed the microRNA (miRNA) expression profile of PCOS with insulin resistance and explored the potential biological functions of differentially expressed miRNA.Methods: A total of 76 patients with PCOS and 30 normal healthy women were recruited in the gynecological clinic of the Second Hospital of Tianjin Medical University. We divided the patients with PCOS into a group with insulin resistance (n=46) and a group without insulin resistance (n=30). Peripheral venous serum samples from each group were used for deep sequencing to identify differentially expressed miRNAs. Hierarchical clustering heat maps were used to show differences in miRNA expression. Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis, and target gene network databases were used to explore the potential target genes of differentially expressed miRNAs and to analyze their specific biological functions.Results: A case-control analysis found that the levels of body mass index (BMI), prolactin (PRL), total testosterone (T), fasting blood glucose (FBG), and fasting insulin (INS) in patients with PCOS were higher than those in healthy controls. High BMI, high blood sugar, and hyperinsulinemia were more significant in the PCOS with insulin resistance group than without insulin resistance group. Among the patients with PCOS, miR-122-5p was found to have more significant differences in the PCOS with insulin resistance group. GO and KEGG pathway analysis showed that the identified miRNAs were involved in the regulation of different biological processes, such as signal transduction, negative regulation of GTPase activity, chloride channel complex. The predicted target genes were related to the citrate cycle (TCA cycle) and the biosynthesis of mucin-type O-glycans.Conclusions: Our research demonstrated the use of miRNAs as new biomarkers for the diagnosis, treatment and presented a new strategy to lessen the symptoms of PCOS with insulin resistance.