Background It aims to evaluate the surgical efficacy and long-term survival of different laparoscopic surgeries for gastric GISTs. Methods From a prospectively collected database, 133 patients with primary gastric GISTs undergoing laparoscopic surgery were selected from January 2008 to December 2014. They were divided into three groups according to the different operations that were performed, including laparoscopic gastric wedge resection (LWR Group, n=103), laparoscopic subtotal gastrectomy (LSG Group, n=18) and laparoscopic total gastrectomy (LTG group, n=12). Clinicopathological features and short- and long-term outcomes were analyzed retrospectively. Results All patients had received R0 resection. There were no differences among the three groups in age, BMI or NIH risk classification. Compared with the LSG group and LTG group, the LWR group had a shorter operative time, less blood loss, fewer operative complications and shorter time to ground activities, semi-liquid diet and hospital stay (P<0.05). There was no statistically significant difference in time to first flatus and liquid diet or in the rate of postoperative complications (P<0.05). In the patients with a large tumor (size≥5 cm), LWR was significantly associated with shorter operative time, less blood loss and shorter hospital stay compared with the laparoscopic gastric non-wedge resection (N-LWR) (P<0.05). The median follow-up was 30 months, with 4 cases of recurrence and 3 deaths. The 5-year cumulative survival rate was similar among the three groups (P>0.05). Conclusions Compared with LSG and LTG, more favorable minimally invasive results can be achieved from LWR for gastric GISTs, which may be the optimal surgical procedure.