BackgroundDental caries and extrinsic black tooth stain (EBS) are prevalent among children, with current evidence suggesting a negative correlation between them. It is unclear whether the factors contributing to developing or preventing dental caries and EBS are connected or aligned.AimTo investigate the prevalence and associated factors of caries and EBS among children with primary, mixed and permanent dentitions.DesignThis was designed as a cross‐sectional study. Probability proportionate to size sampling and simple random sampling methods were used to recruit children aged 5, 9 and 12. Three calibrated paediatric dentists conducted intra‐oral examinations. Nutritional supplements, oral health–related behaviours and family background were collected. Bivariate analysis, negative binomial and binary logistic regression were performed.ResultsCaries and EBS prevalence were 83.7% and 4.7%, respectively. A decreasing trend in caries and an increasing trend in EBS prevalence were observed across three dentitions. Caries were associated with EBS, oral hygiene, vitamin intake, gender, food‐pocketing habits, toothbrushing duration, dental attendance and socioeconomic status. EBS was more likely to occur in caries‐free children (OR = 4.42, 95% CI 2.97,6.58, p < 0.001) and children without vitamin consumption (OR = 1.59, 95% CI 1.07, 2.36, p = 0.021).ConclusionThe occurrence of caries and EBS varied across different dentition stages. Their risk and protective factors were not significantly aligned.