Introduction Polycyclic aromatic hydrocarbons (PAHs) and heavy metals (HMs) are endocrine-disrupting chemicals (EDCs) that may have a combined effect on sex hormone levels in children. This study investigated the correlations between co-exposure to PAHs and HMs and levels of sex steroid hormones in children. Methods We employed the data from the National Health and Nutrition Examination Survey (NHANES) from 2013 to 2016, including 1,167 participants aged 6-19 years. Sex hormone indicators include testosterone (TT), estradiol (E2), sex hormone-binding globulin (SHBG), free androgen index (FAI), and the TT/E2 ratio. Weighted multivariate linear regression, weighted quantile sum (WQS) regression, and Bayesian kernel machine regression (BKMR) were used to analyze the associations between co-exposure to PAHs and HMs and sex steroid hormone levels. Results Co-exposure to PAHs and HMs was associated with a 16.2% reduction [95%CI (-0.321, -0.004)] in SHBG level among prepubertal males and a 16% reduction [95%CI (-0.30, -0.03)] in E2 level among pubertal males by the weighted quantile sum (WQS) regression, and cadmium (Cd) and mercury (Hg) contributed the highest weight respectively. In the Bayesian kernel machine regression (BKMR) model, co-exposure to PAHs and HMs was positively associated with TT/ E2 in pubertal males and negatively correlated with FAI in pubertal females, and 1-hydroxypyrene (1-PYR) and Cd were the most important components respectively. Conclusions Co-exposure to PAHs and HMs was associated with sex hormone levels in children. These findings highlight the necessity for preventing the effects of these chemicals on sex hormones.