Objective To investigate the surgical treatment of gastrointestinal stromal tumor (GIST) based on the clinical characteristics of GIST in different locations. Methods The clinical data of 486 GIST patients who received surgical treatment at the Peking Union Hospital from January 2003 to December 2012 were retrospectively analyzed. There were 461 patients with primary GIST and 25 with secondary GIST.The clinical characteristics and surgical treatment methods were analyzed. All data were analyzed using the chi square test. Results Of the 461 patients with esophageal stromal tumors, 6 received partial esophagectomy. Of the 234 patients with gastric stromal tumors, 183 received partial gastrectomy, 23 received proximal gastrectomy+cardiectomy, 23 received distal gastrectomy,2 received total gastrectomy and 3 received exploratory laparotomy.Of the 51 patients with duodenal stromal tumors,34 received partial duodenectomy,9 received pancreaticoduodenectomy,5 received pyloruspreserving pancreaticoduodenectomy,3 received palliative surgery.Of the 116 patients with small intestinal stromal tumors,110 received partial small intestinal resection and 6 received palliative surgery. Of the 29 patients with rectal stromal tumors, 13 received posterial transsphincteric surgery of the rectum,12 received transanal local resection of rectal tumors and 4 received abdominoperineal resection; laparotomy was performed on 25 patients with GIST in other positions. Of the 25 patients with secondary GIST,10 patients with liver metastasis of GIST received hepatic segmentectomy,1 received hepatobiopsy; 6 received abdominopelvic tumor resection;5 received portial resection of the small intestine or colon;1 received sigmoid colostomy;1 received splenectomy and 1 received intracranial tumor resection.Of the 461 patients with primary GIST, patients who received combined devisceration accounted for 12.58%(58/461), and the ratio of combined cholecystectomy was the highest, which was 34.5%(20/58).Combined devisceration was considered for patients with duodenal stromal tumors, gastric stromal tumors and small intestinal tumors.Laparoscopic surgery accounted for 20.39%(94/461) of all the surgery, and the ratio of laparoscopic surgery which carried out in recent 5 years was 28.52%(77/270), which was significantly higher than 8.90%(17/191) of the earlier 5 years (χ²=36.67, P<0.05).Conclusion Different surgical treatment methods including minimally invasive surgery could be adopted according to different clinical characteristics of GIST in different locations, and radical resection of GIST is the main objective.