In order to assess the association between urinary heavy metals and early childhood caries (ECC), a survey of deciduous tooth decay and urinary heavy metal concentrations of 408 children was conducted in a typical industrial and mining area. The results indicated that urinary heavy metal concentrations were ranked as Zn > Fe > Cu > Pb > Ni > Cd > As > Cr > Mn > Hg. The zero-inflated negative binomial model identified Hg as a significant risk factor for ECC (P25 ~ P75, OR = 3.499; > P75, OR = 3.184). Bayesian kernel machine regression further revealed that Pb, Cd, and Hg were positively correlated with ECC. Additional analysis using the Wilcoxon rank sum test and restricted cubic splines confirmed a positive correlation between the urinary concentrations of Pb, Cd, As, and Hg and the number of ECC (p < 0.05). Moreover, Bayesian kernel function regression and weighted quantile sum regression indicated that combined exposure to heavy metals was positively associated with ECC, with Hg (0.420) being the most dominant contributor, followed by As, Pb, and Cd. In conclusion, this study demonstrated a significant positive correlation between urinary heavy metals and both the occurrence and severity of ECC, with Hg identified as the most influential factor. It was recommended to minimize children's exposure to heavy metals to protect their dental health.