Spontaneous portosystemic shunts(SPSSs) in cirrhotic patients indicate higher incidence of gastric varices, which increases the risk for bleeding and death. However, few studies compared endoscopic therapy with transjugular intrahepatic portosystemic shunt (TIPS) in preventing variceal rebleeding in cirrhotic patients with SPSSs. This research aims to evaluate the effectiveness of the two methods in this group of patients. We reviewed consecutive cirrhotic patients with SPSSs who underwent either TIPS or endoscopic treatment to prevent variceal rebleeding between January 2015 and December 2018 in our institution. Outcomes including rebleeding, overt hepatic encephalopathy (OHE), complications and survival were compared. Meanwhile, subgroup analyses were conducted to screen relevant factors affecting the results. A total of 97 patients were included in the study. The TIPS arm contained 50 patients and the endoscopy arm contained 47 patients. Rebleeding rate in TIPS group was statistically lower than endoscopic group [16.0 vs 38.3%, hazard ratio (HR) = 0.37, 95% confidence interval (CI): 0.16-0.84, P = 0.01], while OHE was more frequent (16.0 vs 2.1%, HR = 7.59, 95% CI: 0.94-61.2, P = 0.025), the survival rate (92 vs 89.4%, HR = 0.88, 95% CI: 0.22-3.60, P = 0.87) and frequency of complications were comparable between two groups. In the subgroups of GOV2/IGV1 and splenorenal shunt/gastrorenal shunt, compared with endoscopic treatments, TIPS reduced the rate of rebleeding without significantly increasing overt hepatic encephalopathy; however, it did not improve survival rate. For cirrhotic patients with SPSSs, TIPS brought a lower rebleeding rate but a higher incidence of OHE. However, in the subgroups of GOV2/IGV1 and splenorenal shunt/gastrorenal shunt, TIPS was considered more reasonable due to the lower rebleeding rate and comparable OHE incidence.