Objective: To investigate the difference in intestinal microbiome between children with atopic dermatitis (AD) and healthy children. Methods: Totally, 35 children with AD were enrolled from the Department of Dermatology, Jiading Hospital of Traditional Chinese Medicine from April 2015 to April 2017, and 27 healthy children served as control group. Total DNA was extracted from the feces of the subjects, and the V3-V4 region of the 16S rRNA gene of the bacteria was amplified by PCR. High-throughput sequencing was performed using the Illumina Miseq sequencing platform to analyze the diversity of bacterial flora. The top 15 abundant bacteria were determined at phylum, genus, and species levels, and compared between the two groups. Statistical analysis was carried out using Wilcoxon rank sum test. Results: The intestinal microbiome in the two groups mainly consisted of Firmicutes, Bacteroidetes, Proteobacteria and Actinobacteria. At the phylum level, the abundance of Bacteroidetes and Fusobacteria was significantly lower in the AD group (29.16% ± 19.96%, 0.06% ± 0.17%, respectively) than in the healthy control group (39.06% ± 15.98%, 0.50% ± 1.71%, respectively, P = 0.042, 0.041) . At the genus level, the abundance of Bacteroides was significantly lower in the AD group (23.77% ± 18.08%) than in the healthy control group (33.1% ± 15.75%, P = 0.029) . There was no significant difference in the distribution of the top 15 abundant species between the two groups (all P > 0.05) . Conclusion There are some differences in the composition of intestinal microbiome and relative abundance of bacteria between children with AD and healthy children.