Abstract:[Objective] This study was conducted to explore the diversity of dietary patterns and gut microbiota among local and immigrant pre-adolescent children in Guangdong province. [Methods] 48 local children and 34 immigrant children in Shenzhen city were randomly selected for food frequency questionnaire survey and morning feces collection. In addition, differences concerning the frequency of dietary intake between local and immigrant children were analyzed by the Mann-Whitney U test and used the Illumina Miseq high-throughput sequencing platform to analyze the gut microbiota. [Results] Among all children, the dietary patterns were mostly rice as the staple food, with vegetables, meat, and fruits. However, the significantly higher intakes of carbohydrates enriched foods, vegetables and seafood in the local group, while significantly higher intakes of fruits, low-fat milk and yogurt in the immigrant group. The immigrant group was associated with increased α-diversity assessed by the Chao1 (P<0.001) and Ace (P<0.001) index. Furthermore, at the genus level, a significant increase in Prevotella and Parabacteroides was observed in the local group (P<0.05). The principal coordinate analysis biplots (ANOSIM, P>0.05) showed no significant changes among the two groups. In addition, the linear discriminant analysis effect size analysis indicated Prevotellaceae (family) and Prevotella (genus) were markedly higher in the local group. The result of redundancy analysis indicated that the intake of vegetables and low-fat milk significantly affected the distribution of intestinal flora in local children, and suggested that the dietary habits of local children may affect the abundance of Prevotella and Parabacteroides. [Conclusion] This study revealed that the differences in diet among local and immigrant children. A significant correlation between the intake of vegetables and low-fat milk and gut microbiota in local children was observed, which provided a new theoretical foundation for understanding the effects of diet on gut microbiota.