Objective To observe the accuracy, safety and efficacy of pinpointing intracranial epileptogenic lesions and guiding surgical treatment of children with refractory epilepsy by using 3D-MRI of cranial brain and venous MRI with contrast enhancement (CE-MRV) into the neural navigation system to form three-dimensional stereoelectroencephalography (SEEG). Methods 22 cases of refractory epilepsy from Mar 2016 to Oct 2017 in our hospital underwent cranial brain 3D-MRI and CE-MRV, which input in StealthViz® neural navigation system to establish stereotactic 3D brain and cortical vein model. Electrodes were implanted and all the brain surface vessels were avoided because of well-designed surgical path under this system. SEEG operations were performed on all patients with surgical indications after intracranial epileptogenic lesions were monitored by long-term video EEG. All patients were followed up after operation to analyze their accuracy, safety and effectiveness. Results 3D-MRI and CE-MRV images of 22 patients were shown clearly, all the electrodes were successfully implanted, A total of 143 electrodes were implanted, none of the cases had complications of bleeding and infection, and the incidence of bleeding was 0%, only one of them was implanted with an electrode in a second operation, and no complications occurred as well. All patients intracranial epileptogenic lesions were localized and removed after monitored by video EEG. Followup effect in all patients were satisfactory. Conclusion Using 3D-MRI of cranial brain and CE-MRV to establish stereoscopic cerebral and cortical venous model can effectively prevent electrode implantation bleeding; SEEG implantation as an invasive method of pre-operation evaluation in refractory epilepsy patients of children is accurate, safe and effective.