Objective To analyze the signs features of ultrasound and multi-slice spiral computed tomography (MSCT) imaging in patients with gastrointestinal stromal tumors (GIST). Methods The clinical data of 68 patients with single GIST diagnosed by surgical pathology (gold standard) underwent ultrasound and MSCT from March 2016 to December 2017 in our hospital were analyzed retrospectively. The differences in the diagnosis of ultrasound and MSCT were compared, and the features of two kinds of examination methods of different malignant risk were analyzed. Results A total of 68 single GIST cases, 41 cases (60.29%) located in stomach, 19 cases (27.94%) in small intestine and 8 cases (11.77%) in rectum. Five cases (7.35%) were extremely low risk, 11 cases (16.18%) were low risk, 14 cases(20.59%) were middle risk and 38 cases (55.88%) was high risk. The accuracy rate of MSCTwas significantly higher than that of ultrasound (P<0.05). The signs features of MSCT and ultrasound towards different risk GIST showed that the higher the risk of GIST was, the larger the tumor diameter was (P<0.05) and the higher the incidence rates of irregular shape and blurring boundary were (P<0.05). But there was no statistical difference in the MSCT calcification and lymph node metastasis between ultrasound and MSCT, ultrasonic echo and blood flow in GIST with different risk degrees (P>0.05). Conclusion MSCT and ultrasound can judge the malignant risk of GIST by evaluating the tumor diameter, shape and boundary, and MSCT can determine the location of GIST more accurately and it is more favorable for the follow-up clinical treatment.