Double-lumen endotracheal tubes and bronchial blockers are the two lung separation devices most commonly used for lung resection. The preference and outcomes of choosing different lung separation devices have not been discussed in the literature. This study was conducted using the data of 2 million patients randomly chosen from the National Health Insurance Research Database between 2011 and 2016. We selected patients who underwent lung resection surgery and surveyed their demographic data and trends of double-lumen endotracheal tube and bronchial blocker use. To determine the influence of endotracheal tubes on clinical outcomes, we computed multiple linear regressions of the number of deaths within 30 days after surgery, intensive care unit stay, hospital stay, and medical cost. The use of bronchial blockers in Taiwan has steadily increased from 6.13% to 11.33% from 2011 to 2016. Anaesthesiologists working in regions with higher thoracic surgery volumes preferred bronchial blockers over double-lumen endotracheal tubes. Bronchial blockers were the preferred choice in women, elderly individuals, patients with more comorbidities, and those undergoing video-assisted thoracoscopic surgeries. After adjustment for sex, age, Charlson Comorbidity Index, and video-assisted thoracoscopic surgeries, we found that patients in whom bronchial blockers were applied had shorter hospital stays. The use of bronchial blockers is increasing as the experience of anaesthesiologists increases. Although double-lumen endotracheal tubes remain the principal choice for lung separation in Taiwan, clinical outcomes of the bronchial blocker group were not inferior to those of the double-lumen endotracheal tube group.