BACKGROUND: There is limited epidemiological evidence on the association between secondhand smoke exposure and growth and developmental problems in children and adolescents. This study aimed to explore the relationship between urinary levels of nicotine, cotinine, and trans-3'-hydroxycotinine and physical health outcomes in Chinese children. METHODS: This cross-sectional study included 491 children aged 8 to 12 years from a primary school in 2023. Socio-demographic characteristics and lifestyle factors, including household routines and caregiver smoking status, were collected through a structured questionnaire. This information was subsequently analyzed to investigate correlations between urinary tobacco metabolite concentrations and physical health outcomes in children. Generalized linear regression models were applied to evaluate the relationships between urinary levels of nicotine, cotinine, and trans-3'-hydroxycotinine and key physical health indicators. RESULTS: Among the 491 children, 168 were classified as overweight or obese, 134 had hypertension, 17 showed abnormal spirometry results, and 394 had low vision. The median urinary concentrations of nicotine, cotinine, and trans-3'-hydroxycotinine were 4.70 ng/mL, 3.91 ng/mL, and 5.33 ng/mL, respectively. After adjusting for potential confounders, urinary nicotine levels were positively associated with weight, body mass index (BMI), systolic blood pressure (SBP), and waist circumference. No significant associations were observed between urinary cotinine or trans-3'-hydroxycotinine levels and physical health indicators. CONCLUSION: Urinary nicotine levels were positively associated with weight, BMI, systolic blood pressure, and waist circumference. In contrast, no significant associations were found between urinary cotinine or trans-3'-hydroxycotinine levels and physical health indicators. These findings suggest that further longitudinal cohort studies are warranted to evaluate the potential of urinary cotinine and trans-3'-hydroxycotinine as reliable biomarkers for assessing and monitoring the physical health status of primary school children.