Objective To compare the efficacy and safety of endoscopic resection and laparoscopic resection of non-minimal gastric stromal tumor (more than 1 cm and less than 5 cm).Methods A retrospective analysis was performed on the clinical data of patient with non microgastric stromal tumor patients which confirmed by pathology and immunohistochemistry after endoscopic resection and traditional open surgery from January 2012 to December 2017. The patients were divided into Endoscopy Group and laparotomy group, compared the hospitalization time, complications and curative resection rate etc between the two groups.Results The postoperative eating time, postoperative exhaust time, hospitalization time of endoscopic resection group were significantly shorter than those of laparoscopic surgery group (P < 0.05), and the hospitalization cost of endoscopic resection group was significantly less than that of laparoscopic surgery group (P < 0.05). The average follow-up time of endoscopic groupwas 32 months, and there was 1 case with recurrence. The average follow-up time of laparoscopic group was 35 months, and there was 1 case with recurrence and 1 case with metastasis, there was no significant difference between the two groups (P > 0.05).Conclusion Endoscopic resection has some advantages for non microgastric stromal tumors with diameters more than 1 cm and less than 5 cm. It has high resection rate, less complications and there was no significant difference in recurrence rate between the two groups.