Gastroesophageal reflux disease (GERD) is closely related to respiratory issues. We reported the case about the nutrition intervention given to a male infant with congenital bronchomalacia, GERD, and recurrent pneumonia. During the first and second pediatric intensive care unit (PICU) stays, his nutrition status and nutrient intake were good. However, during the 18 days of the third PICU admission, his nutrient intake decreased to 75%–80% of his estimated calorie requirement and his Z-score for weight-for-age dropped to −1.4. We conducted nutritional interventions to improve GERD symptoms and nutritional status include avoiding overfeeding by feeding small amounts frequently, using a pre-thickened formula mixed with a high-calorie formula, and feeding through transpyloric tube. As a result, his daily nutrient intakes gradually increased and his Z-score for weight-for-age was normal. In conclusion, it is important to implement individualized intensive nutritional management to ensure adequate nutrition and growth status in infants with lung disease and GERD.