A left-bulging atrial septum (AS) is an abnormal sign indicating hemodynamic overloading of the right heart. We tried to evaluate whether computed tomography (CT)-derived AS bulging and ventricular septum (VS) bowing signs would be used to identify patients with acute pulmonary embolism (PE) and significant hemodynamic derangements. In the prospective registry, 208 consecutive patients with a first episode of acute PE diagnosed by chest CT were grouped by clinical hemodynamic assessment: massive or submassive PE (Group 1), and small PE (Group 2). The curvatures of the AS and VS, and the diameters of right ventricle (RV) and left ventricle were measured on chest CT. Group 1 showed higher degrees of echocardiographic RV dysfunction, and abnormal CT-derived VS and AS curvatures versus Group 2. An abnormal VS bowing sign was observed in 32 (32.7%) and 6 (5.5%) patients in Groups 1 and 2, respectively (P < 0.001). An abnormal AS bulging sign was observed in 59 (60.2%) and 32 (29.1%) patients in Groups 1 and 2, respectively (P < 0.001). An algorithm was designed to predict clinically significant hemodynamic abnormality based on these signs. The patients deemed "higher risk" exhibited higher 90-day all-cause mortality than patients in the lower-risk group (P = 0.029). Conventional chest CT-derived hemodynamic findings, including abnormal AS and VS signs, can be used to identify high-risk patients with acute PE and to predict early mortality.