The interaction between several lifestyle and obesogenic environmental factors is considered as the main underlying factor for the escalating trend of childhood obesity and its adverse consequences. In this study, we assessed the mutual influence of lifestyle habits and body mass index (BMI) as well as risk factors for cardiometabolic, hepatic, and renal disorders to define the causality power of each item. This nationwide cross-sectional study was conducted as the fifth round of a school-based surveillance program. Overall, 14,800 students living in Iran were studied, and blood samples were obtained from 4,200 of them. Demographic factors, anthropometric and biochemical measures were used to define lifestyle-related latent variables as well as cardiac, renal, and hepatic risk indicators. Total, direct, and indirect effects between factors were analyzed using the standardized regression weights for each pathway. Data from 14,274 students (participation rate of 99%) and 3,843 blood samples were included. All of the latent variables had a significant direct effect on BMI, with the most potent effect of unhealthy nutrition (β ≅ 0.63) in boys and girls. BMI has significant direct effects on risk indicators of cardiovascular, renal, and hepatic diseases with the most powerful effect on cardiovascular risk factors (β ≅ − 0.08). The most important predisposing factor for obesity was unhealthy nutrition, whereas increased activity, adequate sleep, and better hygiene had protective roles. BMI shows the strongest association with indicator of cardiovascular diseases. These findings underscore the importance of implementing public health programs for the prevention of chronic noncommunicable diseases.