Objective To compare the performance of four response evaluation criteria，i.e.，RECIST1.1，mRECIST1.1，Choi，and early morphological change（EMC），in predicting the prognosis of patients with gastrointestinal stromal tumors（GISTs） receiving imatinib（IM） treatment，and to investigate the surgical timing of patients with different responses. Methods A retrospective analysis was performed for the contrast-enhanced computed tomography images of 66 patients with GISTs in our hospital before and after IM treatment using the four response evaluation criteria，and the patients were divided into good response group and poor response group based on the response of the first follow-up. The Kaplan-Meier survival curve was used to describe the overall survival（OS） and progression-free survival（PFS） of the two groups based on the four criteria，and the log-rank test was used for comparison of OS and PFS between groups. The proportion of patients with progressive disease（PD） or the best of response（BOR） at different periods of time after treatment were calculated to determine proper surgical timing（under the premise of ≥50% of the patients with BOR and ≤20% of the patients with PD，with the optimal surgical timing defined as the treatment period with the largest difference between BOR and PD）. Results There were significant differences in OS（P=0.043） and PFS（P=0.003） between the good response group and the poor response group according to the EMC criteria，while there was only a significant difference in PFS（P=0.002） between the two groups based on the Choi criteria. The two groups divided based on the RECIST1.1 and mRECIST1.1 criteria were consistent，with no significant differences in OS and PFS between the two groups（P>0.05）. According to the EMC criteria，50% of the patients in the good response group achieved BOR without PD within 1 year after treatment，and the earliest time to PD was 1.5 years after treatment； for the patients with complete response，there was no significant difference in OS between the surgery group and the non-surgery group（P=0.051）. Conclusion The EMC criteria can accurately stratify the prognosis of patients with GISTs in the early stage after IM treatment； according to the EMC criteria，resection can be considered for the patients with complete response after 1 year of treatment，and instead of surgery，these patients may choose more conservative treatment measures such as regular monitoring.