Objective: To assess the clinical application value of 3D laparoscopic surgery in treatment of gastrointestinal stromal tumor in the fundus of the stomach. Methods: The clinical data of 36 patients with gastrointestinal stromal tumor in gastric fundus treated between January 2014 and June 2015 in Renmin Hospital of Wuhan University were retrospectively analyzed. Of the patients, 18 cases underwent 3D laparoscopic resection (3D laparoscopic group) and 18 cases were subjected to open resection (open surgery group). The perioperative variables and postoperative pathological results as well as recurrence and metastasis were compared between the two groups of patients. Results: There were no differences between the two groups in terms of general data such as age, gender, tumor size and BMI (all P>0.05). No statistical difference in operative time was noted between the two groups, while the indices such as intraoperative blood loss, length of the incision, time to postoperative gas passage and length of hospital stay in 3D laparoscopic group were significantly better than those in open surgery group (all P<0.05). No tumor rupture or positive margin was found and no severe complications such as massive hemorrhage, anastomotic fistula and postoperative intestinal obstruction occurred in either group, and the postoperative pathological and immunohistochemical features of the two groups showed no significant difference (all P<0.05). All patients were followed up for 12 to 36 months, and no cases of tumor metastasis and recurrence or death occurred. Conclusion: Using 3D laparoscopic technique in treatment of gastrointestinal stromal tumor in the gastric fundus can significantly minimize the surgical trauma of the patients, and its long-term efficacy is similar to that of open resection.