Objective：To investigate the value of combined trans-abdominal and intraluminal ultrasound on evaluating treatment effectiveness of molecularly targeted drugs in gastrointestinal stromal tumors（GIST）. Methods：A total of 35 patients with GIST confirmed by pathology and immunohistochemistry，who treated with molecularly targeted drugs，were enrolled in this study and their clinical and image data of evaluating the treatment response of targeted drug therapy using both ultrasound and CECT were collected and retrospectively analyzed. According to the response evaluation criteria in solid tumors（RECIST），the coincidence rate and consistency of two imaging methods in evaluating the treatment response of drugs for GIST patients were compared. Results：The consistency of evaluation results of GSIT by two methods of ultrasound and enhanced CT was satisfactory. The Kappa value was 0.821 （P<0.001）. There was no significant difference in evaluation of treatment effectiveness of two imaging methods（P>0.05）. Conclusion：Ultrasound is consistent with enhancement CT for evaluating molecularly targeted drugs in GSIT，which can be an imaging examination method.