Projected to impact 310 million children by the next decade, childhood obesity is linked to serious health issues like metabolic disturbance and cardiovascular diseases. This study introduces a novel approach for the integrated assessment of inflammatory, glycemic and lipid disorders in obese children in resources-limited settings and also identifies key factors contributing to these changes. Conducting a cross-sectional analysis of 231 children aged 5-12 years from public schools in Brazil's semi-arid region, the research involved collecting medical history, anthropometric measurements, and blood samples to analyze glycemic and lipid profiles, along with C-reactive protein levels. We used an adapted the Molecular Degree of Perturbation model to analyze deviations in metabolic markers from a healthy control group. Statistical analyses included Mann-Whitney and Fisher exact tests, backward logistic regression, and hierarchical cluster analysis. The study identified a direct and independent association between elevated Metabolic Disturbance Degree and both overweight and obesity in children, with significant differences in CRP, Triglycerides, and HDL levels noted between obese and healthy-weight groups. The findings highlight the critical need for early detection and comprehensive understanding of obesity-related changes to mitigate the severe health risks associated with childhood obesity.