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Objective: The present study intended to analyze the characteristics of intestinal floral composition and the relationship with serum cytokines in individuals with egg allergy. Methods: A total of 20 subjects were recruited in this study. The abundance and composition of intestinal flora were determined by 16S rRNA gene sequencing, and the serum levels of food allergy-related cytokines such as interleukin-4 (IL-4) and IL-5 were measured by enzyme immunoassay. The differences in the structure of intestinal flora and the levels of cytokines were compared between the egg allergy and control groups and the correlation between them was analyzed. Results: The serum levels of IL-4 and IL-5 were significantly higher in the egg allergy group compared with the control group (P < 0.05). 16S rRNA gene sequencing showed that Betaproteobacteriales, Burkholderiaceae and Eubacterium_hallii group were significantly enriched in the allergy group (P < 0.05). Spearman’s correlation analysis revealed a negative correlation between the abundance of Weissella cibaria and Escherichia and the serum levels of IL-4 and IL-13. However, the abundance of Burkholderiaceae and uncultured_Parasutterella abundance was positively correlated with transforming growth factor beta1 (TGF-β1) and IL-13. Conclusion: This study provides a scientific basis for determining the specific intestinal flora of egg-allergic individuals and for exploring the implication of intestinal flora in preventing or treating egg allergy.