Atrial septal aneurysm (ASA) is a localized deformity of the interatrial septum, which protrudes into the right and/or left atrium. ASA with defects is a source of cardiac embolism. Although transcatheter closure is now a common procedure, it is still challenging in patients with complicated ASA. We describe a case of giant atypical multiperforated ASA with irregular mobility, which showed a rare "aneurysm in aneurysm" structure. Real-time three-dimensional transesophageal echocardiography showed vivid images, which clearly demonstrated these irregular shaped defects mimicking the atriotomy view, and played a crucial role in guiding the transcatheter closure.