Objective To investigate the relationship between vitamin K2,insulin-like growth factor bind-ing protein 3(IGFBP-3),Omentin-1 and the therapeutic effect on children with idiopathic short stature(ISS),and to build a prediction model.Methods A total of 242 ISS children in Jinan Second Maternal and Child Health Hospital from 2019 to 2021 were selected.All of them received recombinant human growth hormone(rhGH)treatment and were divided into effective group and ineffective group according to the therapeutic effect after 12 months of treatment.The general data,vitamin K2,IGFBP-3 and Omentin-1 in the two groups were analyzed.The influencing factors of ISS children's therapeutic effect were analyzed by Logistic regression model and decision tree model.The predictive performance of two models was analyzed by using receiver oper-ating characteristic(ROC)curve.Results There were statistically significant differences in 25-hydroxy vita-min D[25(OH)D],parathyroid hormone(PTH),thyroid stimulating hormone(TSH),vitamin K2,IGFBP-3,Omentin-1,rhGH dosage and weekly outdoor exercise time between the two groups(P＜0.05).Logistic re-gression showed that PTH(OR=7.011,95％CI:2.456-20.014),vitamin K2(OR=0.605,95％CI:.0.465-0.788),IGFBP-3(OR=0.458,95％CI:0.321-0.654),Omentin-1(OR=0.514,95％CI:0.389-0.679)and rhGH dose(OR=0.563,95％CI:0.445-0.712)]were the influential factors for treatment ineffectiveness in ISS children(P＜0.05).The decision tree model showed that vitamin K2,IGFBP-3 and Omentin-1 were the factors influencing the therapeutic effect of ISS,and IGFBP-3 had the most significant impact.ROC curve re-sults showed that the area under the curve of decision tree model and Logistic regression model were 0.922 and 0.908,respectively,with good classification effect.Conclusion The therapeutic effect of ISS children is in-fluenced by factors such as vitamin K2,IGFBP-3,Omentin-1,and so on,and IGFBP-3 has the most significant impact.Logistic regression model and decision tree model could complement each other so as to provide refer-ence for improving the therapeutic effect of ISS children from different aspects.