Background: Surgical resection is the standard treatment for localized and potentially resectable gastrointestinal stromal tumors (GISTs), If the postoperative pathology diagnosis indicates that patients are at high risk of recurrence, they should be treated with imatinib. Even though the introduction of imatinib substantially improved the outcome of GIST patients, it is unclear whether different imatinib treatment regimens affect patients' survival. Methods: This retrospective study included 120 patients who underwent tumor resection for high-risk GISTs between January 2009 and October 2018. The patients were divided into three groups: one group of patients received postoperative imatinib adjuvant therapy regularly (regular treatment group); the second group was not treated with imatinib until they were found to have disease progression (observation group); the third group was treated with postoperative imatinib adjuvant therapy irregularly (irregularly treatment group). The progression-free survival (PFS) and overall survival (OS) were compared between the three groups, and the prognostic risk factors were analysed by the Cox regression model. Results: The median PFS was 45 months (range: 25-59). The 3- and 5-year PFS values were 71.3% and 49.9%, respectively. The PFS in the regular group was longer than in the observation group and irregular group (P<0.001). The median OS was 59 months (range:47-78). The 3- and 5-year OS values were 91.6% and 84.2%, respectively. There were no differences in OS among the three groups (P=0.150). The extent of radical resection (P<0.001) and intraoperative tumor rupture (P=0.005) were independent prognostic factors influencing OS. Conclusions: Irregular administration of imatinib was associated with a worse PFS, but it did not affect the OS of patients with high-risk GISTs. Avoiding intraoperative tumor rupture and R0 resection were associated with better survival.