Objective: To analyze the correlation between 25-hydroxyvitamin D (25(OH)D) and parathyroid hormone (PTH) levels and bone development in children. Methods: 85 healthy children who underwent routine physical examination in our hospital from January 2022 to December 2023 were selected as the research objects. All children received bone mineral density measurement. According to the results, they were divided into the normal skeletal development group (Z value -1–1) and the skeletal dysplasia group (Z value < -1). The clinical general data and laboratory examination results of the two groups were compared. A multivariate logistic regression model was used to analyze the influencing factors of children’s skeletal development. Results: The level of 25 (OH) D in the skeletal dysplasia group was lower than that in the normal skeletal development group, and the level of PTH was higher than that in the normal skeletal development group. There were differences in body mass index (BMI), exercise frequency, eating habits, 25 (OH) D, and PTH between the two groups (p < 0.05). Multivariate logistic regression analysis showed that it was a risk factor for children with skeletal dysplasia (OR > 1). Conclusion: The degree of skeletal development in children is correlated with 25 (OH) D and PTH levels. According to the changes of the above indicators, it can guide the clinical supervision of children’s body mass, establish good diet and exercise habits, and promote the normal development of children’s bones.