Objective To analyze the clinical significance of MSCT in positioning and judgment of risk classification through observing the CT findings of different risks of gastrointestinal stromal tumors (GIST). Methods 60 patients with GIST confirmed by pathology in our hospital between February 2013 and January 2016 were selected as the study objects. According to the pathological results, they were divided into the low risk, moderate risk, high risk of three levels. The CT findings of different risks of patients and CT values were observed and compared. Results In terms of pathological risk classification, the number of cases of low risk, moderate risk and high risk were 30, 17 and 13. The differences in displaying tumor size, density, shape and tumor blood vessels between patients with low risk, moderate risk and high risk GIST were statistically significant (P<0.05). There was no significant difference in pathogenic site, growth pattern and degree of enhancement between patients with different risks of GIST (P>0.05). There were significant differences in plain scan and three-phase enhanced CT values between patients with different risks of GIST (P<0.05). Conclusion There exist typical differences in CT findings of different risks of DIST. The display of tumor size, density, shape and tumor blood vessels contributes to risk classification, which provides the basis for the development of clinical treatment and evaluation of prognosis.