Objective To compare the levels of 25-hydroxyvitamin D[25-(OH)D] in children with growth hormone deficiency (GHD) and idiopathic short stature (ISS), and to study its relationship with the growth hormone/insulin-like growth factor-1 (GH/IGF-1) axis. Methods A total of 138 children with GHD and 199 children with ISS were selected. The levels of 25-(OH)D and the proportion of vitamin D deficiency were compared between the two groups. The correlation factors of 25-(OH)D in children with short stature were analyzed, and a multivariate linear regression model with IGF-1 as the dependent variable was established. Result sThe level of 25-(OH)D in GHD group was higher than that in ISS group, and the difference was statistically significant (P<0.05). The proportion of 25-hydroxyvitamin D deficiency and insufficiency in ISS group was higher than that in GHD group, the difference was statistically significant (χ ² = 5.966, P=0.015). 25-(OH)D was negatively correlated with age, body mass index (BMI), IGF-1, insulin-like growth factor binding protein-3 (IGFBP-3) and growth hormone peak (GHpeak) (P<0.05), and positively correlated with bone age index (BAI)(P<0.05). There was no correlation with gender (P>0.05). Multivariate linear regression model showed that age, BMI and BAI were the influencing factors of IGF-1 (P<0.05), while 25-(OH)D did not constitute the influencing factors of IGF-1 (P>0.05). Conclusion Insufficient or deficient vitamin D is common in ISS and GHD children, especially in ISS children. 25-(OH)D does not constitute a factor in the GH/IGF-1 axis in children with short stature, and routine vitamin D supplementation is recommended for GHD and ISS children, but not as an alternative to recombinant human growth hormone therapy.