Polycystic ovary syndrome (PCOS) is a complex class of endocrine disorders with insulin resistance, compensatory hyperinsulinaemia and obesity. However, the pathogenesis and therapies of PCOS have not been fully elucidated. Exosomal miRNAs have the potential to serve as biomarkers and therapies for a wide range of medical conditions. In this study, we isolated exosomes from follicular fluid collected from 5 PCOS patients and 5 non-PCOS patients. miRNA cDNA library sequencing identified 124 miRNAs that were significantly upregulated nearly twofold, while 33 miRNAs were significantly downregulated nearly twofold in PCOS follicular fluid exosomes. These miRNA target genes were mainly involved in metabolic pathways, pathways in cancer, the PI3K-Akt signalling pathway, the MAPK signalling pathway, endocytosis, the Ras signalling pathway, the Hippo signalling pathway, and cellular senescence. According to the previously reported exosomal lncRNA data of PCOS follicular fluid, a miRNA and lncRNA coexpression network developed from data from starBase strictly screened 29 differentially expressed miRNAs. This network also helped to identify miRNA signatures associated with metabolic processes in PCOS. Collectively, these results demonstrate the potential pathogenesis of PCOS, and follicular fluid exosomal miRNAs may be efficient targets for the diagnosis and treatment of PCOS in long-term clinical studies.