Abstract Objectives To investigate the characteristics of pharyngeal and laryngeal structure in patients with acquired brain injury (ABI), who were long time wearing nasogastric tube (NGT) with or without tracheostomy. Methods 103 ABI patients with NGT indwelled for more than 1 month were retrospectively studied and divided into two groups by whether or not undergoing tracheostomy. Age, gender, types of brain injury, course of the disease, disorders of consciousness, activities of daily living (ADL) and fiberoptic endoscopic examination of swallowing (FEES) were evaluated. The structure and function of pharyngeal and laryngeal were assessed by FEES, focusing on the morphology of the arytenoid cartilage, epiglottis, vocal folds, tongue base, and pharyngeal cavity. Results Prolonged indwelling nasogastric tubes and tracheostomy tubes might lead to abnormal alterations of the structure and function in the arytenoid cartilage, epiglottis, tongue base, and pharyngeal cavity. Epiglottis shape abnormality, glossoptosis and pharyngeal stenosis were present in a larger proportion of the NGT–TRACH (nasogastric tube with tracheostomy) group than the NGT group (p