IgA nephropathy (IgAN) is one of the most common causes leading to end-stage renal failure. The regulatory mechanisms underlying the emergence of microRNA are poorly understood and need to be studied for developing better strategies for diagnosis and treatment of pediatric IgA nephropathy. We performed a microRNA sequence analysis of the plasma microRNAs of pediatric patients with IgA nephropathy and healthy control by next generation sequencing (NGS) using the Illumina Deep Sequencing technology. We obtained 18,395,453, 11,348,541 and 22,646,434 qualified Illumina reads from three healthy controls, or 4,287,101, 5,473,799, 5,598,305, 7,713,565, 3,766,914, 7,249,629, 4,199,660, 5,623,320 and 3,014,665 qualified Illumina reads from nine pediatric patients, respectively. Comparative microRNAs analysis differentially revealed 2591 microRNAs between pediatric patients and healthy controls, one expression of microRNA was up-regulated and 19 expressions of microRNA were downregulated. The volcano plot was used to further identify differential microRNAs expression between the two groups. Cluster analysis was performed, and spearman correlation coefficient was calculated and analyzed. Gene ontology (GO) consortium and data were used to analyze the targets gene of different microRNAs. Our work demonstrated differential microRNAs between pediatric patients and healthy controls. Numbers of microRNAs will serve as a promising resource for revealing the regulatory molecular mechanisms of expression associated with the pathophysiology and pathogenesis of IgAN, even their implications in the field of therapy.