This study investigated the effect and safety of targeted embolization in partially embolized cerebral arteriovenous malformation (AVM) followed by gamma knife surgery (GKS). We retrospectively analyzed 86 AVM patients who were targeted embolized by Onyx followed by GKS for residual nidus. Embolization-related complications were collected and the clinical effect was evaluated. During targeted embolization, intranidus or hemodynamic aneurysms and AVM-related fistula were evaluated and targeted embolized. Patients with AVM-related aneurysms and fistula were divided into a targeted embolization group and non-targeted embolization group based on the retrospectively determined treatment strategy. The effect of targeted embolization on hemorrhage risk was evaluated. The overall annual hemorrhage rate was 1.66% with 2.26% for ruptured AVMs and 1.08% for unruptured lesions. The annual mortality rate was 0.4%. Only one in 16 patients with embolization-related complications had permanent neurologic deficit. Twenty-four of 29 cases with intranidus aneurysms were targeted embolized, four of five cases with hemodynamic aneurysms were targeted embolized and eight of nine cases with arteriovenous fistula were targeted embolized. Chi square results showed the hemorrhage complications in the target embolization group were significantly lower than those in the non-target embolization group (p < 0.01). Targeted embolization combined with GKS treatment decreased the annual hemorrhage rate and improved clinical outcome with low permanent complications in partially embolized AVMs. This method could be proposed for the treatment of large brain AVMs when a single-technique treatment is not feasible.