Objective To analyze the correlation of BMI based nutritional status with serum insulin-like growth factor-1 (IGF-1), insulin-like growth factor binding protein-3 (IGFBP-3), vitamin D (25-hydroxyvitamin D, 25 (OH) D) and bone age in children with short stature. Methods A total of 663 children aged 4-10 years old with short stature who were admitted to the Growth and Development Clinic of Shanxi Children's Hospital from June 2019 to August 2023 were selected as the study subjects. Their BMI values were calculated, and according to the BMI standard deviation unit growth curve of Chinese children aged 0 to 18 years, they were divided into four groups: emaciated, normal, overweight and obese. The differences of serum indexes ［IGF-1, IGFBP-3, 25(OH)D］ and bone age among all groups were compared, and the correlation between BMI and serum indexes and bone age was analyzed. Results Serum levels of IGF-1 and IGFBP-3 were positively correlated with BMI in children with short stature (r=0.224, 0.216, both P<0.05), 25(OH)D level was negatively correlated with BMI (r=-0.113,P<0.05). Serum levels of IGF-1 and IGFBP-3 increased successively in emaciated, normal, overweight and obese children with short stature, and there was no significant difference between the overweight and obese groups, and the differences among the other groups were statistically significant (P<0.05), serum 25(OH)D levels decreased successively, but the difference was not statistically significant (P>0.05). Bone age and bone age difference (BAD) were positively correlated with BMI (r=0.175, 0.085, P<0.05). The bone age of emaciated, normal, overweight and obese children with short stature increased successively, but only the difference between obese group and the other three groups was statistically significant (P<0.05). The BAD of emaciated, normal, overweight and obese children decreased successively, but only the differences between emaciated group and overweight group, emaciated group and obese group，normal group and obese group were statistically significant (P<0.05).Conclusion Nutritional status can affect serum IGF-1 and IGFBP-3 levels and bone age in children with short stature, but the effect on 25(OH)D level may not be obvious. In clinical practice, when applying IGF-1, IGFBP-3 and bone age to assess the growth and development of children with short stature, considering the influence of nutritional status can make diagnosis and treatment more accurate and avoid waste of medical resources