Early life stress (ELS), such as neglect and maltreatment, exhibits a strong impact on the mental and brain development of children. However, it is not fully understood how ELS affects the body and behavior of children. Therefore, in this study, we performed social isolation on weaned pre-adolescent mice and investigated how ELS could affect gut microbiota and mouse behavior. Using the metagenomics approach, we detected an overall ELS-related change in the gut microbiota and identified Bacteroidales and Clostridiales as significantly altered bacterial groups. These metagenomic alterations impaired social behavior in ELS mice, which also correlated with the abundance of Bacteroidales and Clostridiales. Our results demonstrate that ELS alters the gut microbiota and reduces social behavior in adolescent mice.