Objective: To fully evaluate the relationship between the Ki-67 and the clinicopathologic feature of gastrointestinal stromal tumor (GIST) patients and the prognostic value of Ki-67 index in GIST patients. Methods: Clinical data of 90 GIST patients who were undergone surgical treatment from January 2013 to August 2017 in the Department of Gastrointestinal Surgery Xiangya Hospital of Central South University were reviewed retrospectively. The immunohistochemical of Ki-67 was detected at the Department of Pathology of Xiangya Hospital. The receiver operating characteristics (ROC) curves were constructed according to the Ki-67 index and the modified the National Institutes of Health (NIH) criteria grade to acquire the cut-off value of Ki-67 index. We classified the GIST patients into low Ki-67 group or high Ki-67 group according to the cut-off value. The clinicopathologic feature and progression free survival rates (PFS) were analyzed between the two group. Results: The cut-off value of Ki-67 index was 2.5%, the sensitivity was 0.783 and the specificity was 0.667. Compared with low Ki-67 index group, high Ki-67 index group patients have bigger tumor diameter (P=0.002), more mitotic count (P<0.001). There was no significant difference in gender, age, tumor site, CD117, CD34, and Dog-1. The tumor site, tumor size and Ki-67 index are the poor independent prognostic factors of GIST patients. The median follow-up time was 18 months (from 5 to 59 months). During the follow-up time, 8 patients were found to have recurrence or metastasis. The PFS of 48 months of high Ki-67 index group was shorter than the low Ki-67 index group (75.8% vs 100%, P=0.017). Conclusion: Ki-67 index can be an important reference index of evaluation of GIST patients’ prognosis and it is related to the tumor size, the mitotic count and the modified NIH criteria grade.