To dig the clinical significance of micro-RNA and mRNA changes under hand, foot, and mouth disease (HFMD) virus infection, we conducted this bioinformatics analysis to clarify crucial differentially expressed genes (DEGs), functional and pathway enrichment, and the relative regulatory network, using four published datasets. Following datasets form GEO database were used for analysis: GSE85829, GSE94551, GSE52780 and GSE45589. After screening of common differentially expressed miRNAs (DE-miRNAs), five key miRNAs were acquired: miR-100-3p, miR-125a-3p, miR-1273g-3p, miR-5585-3p, and miR-671-5p. Based on above five key miRNAs, GO functional and KEGG pathway enrichment were performed using the miRPath V3 database. there were three common enriched GO terms between miRNA-derived prediction and mRNA-derived (dataset GSE45589) analysis: biosynthetic process, cytosol, and nucleoplasm. And one common KEGG pathway, cell cycle, was shared between miRNA-based and mRNA-based enrichment. Using TarBase V8 in DIANA tools, we acquired 1520 potential targets (mRNA) from the 5 key DE-miRNAs, among which 11 DEGs were also included by the159 DE-mRNAs. These common DEGs showed a PPI network mainly connected by SMC1A, SMARCC1, SF3B3, LIG1 and BRMS1L. Together, changes in 5 key miRNAs and 11 key mRNAs may play crucial roles in HFMD progression. Our results shed light on the crucial roles of these DEGs and several functions/pathways in HFMD. Combination of these roles may benefit the early diagnose and treatment of HFMD.