A man in his early twenties with obesity was found dead in his apartment. The deceased was found naked and surrounded by empty bottles of electrolytes. An autopsy performed approximately 6 days postmortem and gross inspection revealed the absence of injury and no apparent extrinsic cause of death. It was decided to dissect to investigate the cause of death. The deceased had become morbidly obese (weight, 98 kg; height, 160 cm; body mass index, 38.3). Shortly before his death, he presented at a clinic complaining of gastric discomfort and heartburn, but other than hypertension (155/91 mmHg) no specific abnormality was found. He was normothermic (36.6℃), and his blood oxygen saturation was normal (97%). Postmortem computed tomography of the thorax revealed a mediastinal mass obstructing the trachea, an upper-airway obstruction, and a narrowed thoracic cavity due to upward compression by an enlarged fatty liver. Autopsy confirmed that the tracheal mass was fatty tissue within the thymus and that upward pressure from an enlarged fatty liver had compressed the thoracic cavity. The deceased likely developed nocturnal chronic hypoxia because of compression by the mediastinal fat mass as well as intermittent hypoxia because of obstructive sleep apnea when lying supine. Chronic and intermittent hypoxia, diabetes, and obesity activate the sympathetic nervous system, increasing the risk of hypertension, heart failure, and arrhythmias. Histological findings showed pulmonary congestion and edema, reflecting heart failure as well as myocardial fragmentation and waving, showing hyper-contraction and hyper-relaxation, respectively. Hypertension, feeling overheated, and myocardial hyper-contraction can be explained as sympathetic nerve over-activation. Intra-cardiac coagulation and a renal cortical pallor suggested subacute death from cardiogenic shock due to heart failure. Postmortem computed tomography before autopsy detected airway obstruction and revealed the cause and pathophysiology of unexpected death in a young man with morbid obesity. Therefore, this could be a potentially useful clinical practice for determining the cause of death postmortem.