Objective To explore a scoring system of preoperative evaluation for high-risk gastric stromal tumors. Methods A total of 275 consecutive patients with gastric stromal tumors of diameter ≤5 cm who underwent surgical or endoscopic resection at Xijing Hospital between 2008 and 2018 were retrospectively enrolled in the study. Multivariate logistic regression analysis was performed to investigate independent risk factors for high-risk gastric stromal tumors.Weighted points was proportionally assigned based on β regression coefficient value to establish the scoring system. The receiver operator characteristic (ROC) curve was plotted, the scoring system as the test variable, and the area under curve (AUC) was calculated. Results Multivariate analysis revealed tumor size＞1.75 cm (OR=6.474, 95%CI： 2.335-17.948), irregular tumor shape (OR=3.548, 95%CI： 1.745-7.216) and mucosal ulceration (OR=2.412, 95%CI： 1.154-5.041) were independent risk factors for high-risk gastric stromal tumors of diameter ≤5 cm (P＜0.05). These risk factors for high-risk gastric stromal tumors were weighted with value: one point for mucosal ulceration, two points for irregular tumor shape and three points for tumor size＞1.75 cm. The AUC value of the scoring system was 0.781, of which the cut-off value was 4. According to the cut-off value, 0-3 points was categorized as the low risk group and 4-6 points as the high risk group for gastric stromal tumors. The incidence of high-risk gastric stromal tumors of the low risk group and the high risk group were 13.3% (26/196) and 48.1% (38/79), respectively, with significant difference (χ2=38.266, P＜0.001). Conclusion Tumor size larger than 1.75 cm, irregular tumor shape and mucosal ulceration can be applied to establish a preoperative scoring system to predict high-risk gastric stromal tumors of diameter ≤5 cm.