Background: The differentiation between Growth Hormone Deficiency (GHD) and Idiopathic Short Stature (ISS) primarily relies on the growth hormone stimulation test (GHST),which is invasive and can cause adverse effects. Objective: To evaluate the diagnostic value of bone turnover markers in distinguishing GHD from ISS. Methods: A cross-sectional study was conducted, enrolling 76 children aged 3-11 years with short stature (37 in the GHD group and 39 in the ISS group). Clinical data including height, weight, bone age, Insulin-like Growth Factor 1(IGF-1), and Peak Growth Hormone (GHP) levels were collected. Eight bone turnover markers were measured: Osteocalcin (OC), beta-C-terminal telopeptide of type I collagen (beta-CTX), 25-Hydroxyvitamin D (25(OH)D), Vitamin D (VitD), Alkaline Phosphatase (ALP), Parathyroid Hormone (PTH), serum Calcium (Ca), and serum Phosphorus (P). Nonparametric tests were used for intergroup comparisons. Logistic regression and Receiver Operating Characteristic (ROC) curve analyses were performed to assess diagnostic efficacy, and Spearman correlation analysis was employed for correlation evaluation. Results: The OC level in the GHD group was significantly lower than that in the ISS group (P < 0.001), while serum P was higher in the GHD group (P < 0.05). Multivariate analysis identified OC as an independent discriminative factor (OR = 182.585, P < 0.001). ROC curve analysis revealed that OC had an area under the curve (AUC) of 0.949, At a cutoff of 1.026 ng/mL, sensitivity was 86.49% and specificity was 100%. Correlation analysis indicated a positive association between OC levels and GHP (r = 0.6, P < 0.05). Conclusion: Serum OC shows high diagnostic value for distinguishing GHD from ISS, demonstrating significant clinical utility.