Abstract: OBJECTIVE To evaluate the efficacy and safety of the molecular targeted therapeutic drugs for gastrointestinal stromal tumors treatment. METHODS Databases including Pubmed, Embase, Web of Science and China National Knowledge Infrastructure (CNKI) were searched for randomized controlled trials of molecular targeted GIST treatment study. The software adopted was RevMan 5.3. The experimental group were treated with different receptor kinase inhibitors (imatinib, sunitinib, regorafenib, nilotinib and pazopanib). While the control group were given by placebo or best supportive care. The primary endpoint of this study included progression-free survival (PFS), overall survival (OS) and grade 3-4 adverse events (AE). RESULTS Seven randomized controlled trials were selected, with 1 528 patients. Overall improvement was significant for PFS(HR=0.34, 95%C1 0.26-0.44, P<0.001), OS (HR=0.38, 95%CI 0.17-0.85, P<0.02). Grade 3-4 AEs with a significantly increased incidence included(neutrophil reduction, hypertension, hand and foot syndrome, rash, diarrhea and fatigue) (RR=4.47, 95%CI:2.12-9.39, P<0.000 1). CONCLUSION Overall, molecular targeted therapeutic drugs were effective in advanced or metastatic GIST patients by improving the PFS and OS. Although the rate of AE is higher compared to the control group, the toxicity is limited.