This study explores the clinical application value of percutaneous endoscopic gastrostomy (PEG) in children with dysphagia after brain injury. Children with dysphagia after brain injury were selected and randomly divided into a treatment group and a control group using a random number table method, with 42 cases in each group. The control group received nutritional support using indwelling nasogastric tube technology, while the treatment group received nutritional support using PEG technology. Both groups received the same tube feeding nutrient solution. At the same time, both groups of patients received comprehensive training methods including oral sensation training, oral exercise training, and physical therapy for swallowing dysfunction. Weight, total serum protein, serum albumin, and hemoglobin of the patients were measured 1 day before treatment and 28 days after treatment, respectively. The degree of dysphagia was evaluated by the water swallow test and the dysphagia disorders survey of each patient 1 day before treatment and 28 days after treatment, respectively. Adverse events such as gastrointestinal bleeding, aspiration pneumonia, and reflux esophagitis were recorded. After 28 days of treatment, both the control group and the PEG group showed an increase in body weight, total serum protein, serum albumin, and hemoglobin compared to before treatment (P < .05), and the PEG group showed a more significant increase than the control group (P < .05). At the same time, swallowing function improved more significantly in the PEG group (P < .05), and the incidence of adverse events was lower compared to the control group (P < .05). The comprehensive training method for swallowing disorders combined with enteral PEG nutrition has a definite effect on children with swallowing disorders after traumatic brain injury.