BACKGROUND: Childhood is an important window for early identification of health risk factors, shaping health behaviors, and preventing future chronic diseases. As a major risk factor, low physical activity (PA) is currently highly prevalent among children worldwide. Meanwhile, long-term low PA has been shown to be associated with short-and even long-term poor health outcomes. Therefore, this study first analyzed the association of low PA with some early chronic disease predictors, followed by further sex-stratified analysis. METHODS: This study used cross-sectional survey data from the National Health and nutrition examination between August 2021 and 2023 August. The Functioning Questionnaire, Global Physical Activity Questionnaire and self-assessment questionnaire were used in the investigation, and metabolic parameters were assessed according to the results of biochemical examination and human body morphological measurements. Binary logistic analysis and linear regression was used to analyze the relationships between PA and chronic disease predictors and their sex stratification. RESULTS: The mean age of the 3 957 participants was 8.94 years (SD = 1.15), and 1 940 (40.0%) were girls, 2 017 were boys. Chi-square analysis showed that girls had lower levels of PA, boys had lower memory, adaptability, self-control and sociability, and girls were more likely to suffer from depression and anxiety, high-density lipoprotein (HDL) was higher in girls than boys (all < 0.05). On multivariate analysis, boys' lower PA was associated with lower sociability, higher HDL, greater waist circumference (WC), and higher body mass index (BMI). Lower PA in girls was associated with lower self-control ability, higher hypersensitive C-reactive protein (H-CRP), higher WC, and higher BMI. CONCLUSIONS: The lower the level of PA of children is, the higher the health risk of cognitive function and metabolic parameters, and these association differ by sex. On the basis of this difference, targeted interventions can be proposed to reduce the burden of disease in the future. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12889-025-24321-8.