Objective To construct regulatory network of dysregulated miRNAs and mRNAs in endometriosis and explore its molecular pathogenesis based on bioinformatic analysis. Methods GSE7305 was download from GEO and conducted with difference expression genes (DEGs) analysis using R software. Endometriosis-related miRNAs were obtained via HMDD V3.0 according to the reported frequency (≥2) and target mRNAs were predicted by miRwalk 2.0. These predicted target mRNAs were intersected with DEGs (|log2 FC| ≥2, P?≤?0.05) in GSE7305 and upon a matching analysis, miRNA-mRNA interaction pairs were acquired. Finally, miRNA-mRNA regulatory network was mapped by Cytoscape software and plugin cytohubba was applied to screen hub miRNAs and mRNAs, resulting in corresponding subnetworks. Result Total of 655 DEGs were obtained from GSE 7305 and most of them were enriched in complement and coagulation cascades pathway, p53 signaling pathway, Cell adhesion molecules (CAMs) pathway. In the established miRNA-mRNA regulatory network, hub downregulated miRNAs including hsa-miR-20a-5p, hsa-miR-141-3p, hsa-miR-200b-3p, hsa-miR-449b-3p all could regulate target gene GATA6. In addition, hub upregulated miRNA hsa-miR-125-5p could downregulate PGR and ESR1. Conclusion Establishment of miRNA-mRNA regulatory network through chip analysis and database mining provided new sight for exploring molecular pathogenesis as well as a combined biomarker based on miRNA-mRNA pairs in endometriosis.