Objective To compare the accuracy of different auxiliary examinations in the diagnosis of intestinal stromal tumor site and size, and analyze the correlation between postoperative pathological risk and clinical indicators. Methods A retrospective analysis was performed on 21 cases of small intestinal stromal tumor diagnosed by pathology after single balloon colonoscopy and CTE in the Second Affiliated Hospital of The Army Military Medical University between January, 2017 and October, 2020. The accuracy of intraoperative diagnosis of tumor site and size was compared with colonoscopy and CTE, and the correlation between pathological risk and clinical manifestations, age and gender was analyzed. Results Twenty-one patients met the inclusion criteria, including 16 cases of hematochezia(76.2%) and 5 cases of abdominal pain(23.8%). Their age was 23～78 years, with average age of(53±15.31) years, most of the small intestinal stromal tumors were located in the upper jejunum. There was statistical significance between the tumor size measured by colonoscopy and CTE and the intraoperative size(P＜0.05), but CTE was superior to colonoscopy in the diagnosis of tumor size. Univariate analysis showed that pathological risk degree was significantly correlated with age, hemoglobin, symptoms(P＜0.05). Conclusion Small intestinal stromal tumors are most common in the upper jejunum. In the auxiliary examination of CTE, the tumor size measured by colonoscopy was smaller than the true value, and CTE was closer to the true value compared with colonoscopy. Pathological risk is related to age, clinical symptoms, and bleeding degree.