Background: Children with precocious puberty are often at an elevated risk for conditions like hypertension, obesity, diabetes and infertility. Some studies suggest a correlation between precocious puberty and dental development, including dental maturity, dental age and malocclusion. However, the relationship between precocious puberty and tooth number anomalies remains largely unexplored. Here, we investigate the link by analyzing two distinct populations. Methods: A total of 253 children were recruited using convenience sampling and categorized into two primary groups based on predefined inclusion and exclusion criteria: Group A (69 with tooth number anomalies, 56 without) and Group B (65 with precocious puberty, 63 without). Results: The results show that children with precocious puberty had significantly higher prevalence rates of tooth number anomalies and increased height, weight and body mass index (BMI) compared to those without (p < 0.05). Among children with precocious puberty, those with tooth number anomalies exhibited significantly higher levels of luteinizing hormone (LH) and follicle-stimulating hormone (FSH) compared to those without anomalies (p < 0.05). However, there are no significant differences in height, weight, BMI, LH or FSH levels between children with and without tooth number anomalies (p > 0.05). Further analysis showed that the independent risk factors for precocious puberty included sleeping with lights on, absence of a napping habit, low paternal education level, lack of intimacy with the father, frequent consumption of out-of-season fruits and fried foods, and maternal menarche before the age of 13 years. (Odds Ratio (OR) = 0.285, 2.971, 1.741, 2.085, 0.228, 0.266, 0.277; p < 0.05). Conclusions: Overall, this study indicates that children with precocious puberty have a higher prevalence of tooth number anomalies. Environmental, dietary, familial and genetic factors may influence the onset and progression of precocious puberty. Early assessment and timely intervention for tooth number anomalies in these children are crucial for their development.