Objective:To reveal the expression and regulation network of microRNA (miRNA) and mRNA in ovarian endometriosis using high-throughput sequencing, and then explore the potential pathogenesis.Methods:From January 2017 to January 2018, twenty patients with ovarian endometriosis in Xiangya Hospital of Central South University were enrolled. Ectopic endometrium and paired eutopic endometrium were collected when surgery was conducted. After total RNA was extracted, miRNA sequencing and mRNA sequencing were performed respectively. Differential miRNA and mRNA expression profiles were analyzed. Predicted mRNA were obtained by Targetscan and miRDB databases, and then intersected with differential mRNA to obtain candidate mRNA. miRNA-mRNA regulatory network was analyzed using Cytoscape software, whereas gene ontology (GO) and pathway function enrichment were performed by DAVID database.Results:Compared with eutopic endometrium, there were 369 miRNAs (197 up-regulated, 172 down-regulated) and 3 765 mRNAs (1 975 up-regulated and 1 790 down-regulated) differentially expressed in ectopic endometrium. Real time quantitative polymerase chain reaction (qRT-PCR) confirmed that the expression of mir-202-5p and mir-514a-5p in ectopic endometrium was higher than that in eutopic endometrium ( P<0.05), while the expression of mir-375-3p, mir-449b-5p in ectopic endometrium was lower than that in eutopic endometrium ( P<0.05). Bioinformatics found that the candidate mRNA related to these four miRNAs are mainly enriched in biological processes of nuclear steroid hormone receptor binding, transmembrane receptor and protein kinase activity, and participate in transforming growth factor β (TGF β) signal pathway, adhesion junction, Wnt signal pathway and Rap1 signal pathway. Conclusions:miRNA and mRNA are differentially expressed in endometriosis, and exact important regulatory network in the development of endometriosis by involving multiple biological processes.