Tuberous sclerosis complex is a multisystem genetic disorder characterized by the growth of numerous tuberous lesions in brain. However, few in vivo studies on TSC have focused on venous structure changes, their association with TSC lesions, and iron accumulation in basal ganglia. 7T susceptibility weighted imaging was performed on eleven TSC patients in comparison with fifteen age- and sex-matched healthy controls. The tubers might develop along penetrating veins. There might be coexistence of iron deposition and calcification in basal ganglia. These in vivo 7T MRI findings provided new perspectives for better understanding the brain pathology in patients with TSC.