This study investigated the impact of bronchoscopic lung volume reduction treatment using endobronchial valves (EBV) on diaphragm configuration. We successfully analyzed the diaphragm index using a newly developed quantitative computed tomography (QCT) tool before and after EBV treatment in forty patients with severe emphysema. We evaluated whether changes in the diaphragm index were associated with improvements in forced expiratory volume in one second (FEV1), residual volume (RV), Saint Georges Respiratory Questionnaire (SGRQ), and 6-minute walking distance (6MWD) using Spearman’s rho. The EBV treatment influenced the diaphragm configuration only on the treated side, resulting in an increased diaphragm curvature. There were significant associations of relative diaphragm index changes on the treated lung side or the entire diaphragm with improvements in FEV1 and 6MWD. These findings provide valuable insights into how EBV treatment affects the diaphragm in COPD patients.