Conventional methods, such as dietary adjustments and exercise training, are pivotal in managing body weight and influencing the gut microbiota. However, the complex interactions among these factors in controlling obesity remain unclear. This pilot study explored the short-term effects of combined exercise and dietary intervention on body mass index (BMI) and gut microbiota composition in obese children. By evaluating changes in both body composition and gut microbiota before and after the intervention, this study provides valuable insights into the synergistic impact of diet, exercise, and microbiome modulation on pediatric obesity. Methods: Publicly available data of 16S amplicon-sequencing from a cohort of obese Chinese infants have been explored with metagenomics analysis tools in this study. A six-week multidisciplinary intervention was conducted with twenty-four obese Chinese children aged 9–13 years, all with a BMI at or above the 97th percentile. The participants were categorized into three groups: Girls (n = 12), Boys (n = 12), and Mixed-gender (n = 12). Anthropometric measurements, including BMI and metabolic parameters (fasting blood glucose, triglycerides, LDL cholesterol), were taken before and after the program, which consisted of five weekly sessions. Additionally, fecal samples were collected at the beginning and end of the intervention, and their extracted DNA was analyzed by sequencing the V3-V4 hypervariable regions of the 16S rRNA gene. Microbial diversity and abundance were evaluated via QIIME software. Results: The intervention significantly reduced BMI for girls, from 69.43 to 60.62 kg/m2, whereas boys experienced a slight increase from 64.14 to 68.86 kg/m2. The metabolic parameters improved notably, with decreases in fasting blood glucose (from 4.37 to 4.14 mmol/L; p = 0.014), serum triglycerides (from 4.15 to 3.25 mmol/L; p < 0.001), and LDL cholesterol (from 2.30 to 1.73 mmol/L; p < 0.001). Microbiota analysis revealed a decrease in Bacteroides plebeius and Faecalibacterium prausnitzii in girls and a reduction in Bacteroidetes vulgatus with increased Prevotella PAC001304_s in boys. Boys presented greater alpha diversity (3.38) than girls did (3.18), with greater variability in beta diversity. These results suggest that combined dietary and exercise intervention has a significant effect on both BMI and the gut microbiota composition in the short term. Conclusions: The six-week intervention effectively reduced BMI and improved metabolic parameters in obese girls but had a less pronounced effect on obese boys. The observed shifts in the gut microbiota emphasize the potential benefits of combining dietary and exercise interventions in managing pediatric obesity and highlight the need for sex-specific adjustments to increase overall effectiveness.