Environmental chemicals can affect the composition and metabolic functions of gut microbiota, leading to various diseases including obesity. The composition of gut microbiota is highly dynamic in the early stages of life. Increasing lines of evidence suggest the adverse effect of early onset chemical exposure on gut microbiota and adulthood body weight gain. Paraquat (PQ) is a widely used toxic herbicide. However, it remains unclear whether PQ can affect the gut microbiota, particularly exposed during early life stage and its link to obesity in adulthood. Here, we applied 16S rRNA gene sequencing to explore how the gut microbiota of adult mice changed after postnatal PQ exposure via intraperitoneal injection. In addition, the body weight of mice was monitored through adulthood. Our results showed that early-life PQ exposure increased the body weight and perturbed the gut microbiota of adult mice in a highly sex-specific manner. In males, early PQ exposure reduced gut microbiota diversity and altered the structure of gut microbiota in adulthood. Interestingly, these changes were not observed in females. Moreover, gene function prediction analysis implied that PQ-induced alteration of gut microbiota was highly correlated with body weight gain in male mice. Taken together, these results suggest that early-life PQ exposure can perturb the gut microbiota and result in increased body weight in adult male mice, which highlights the potential role of gut microbiota in the toxicity of early-life PQ exposure and its sex-specific effects.