In Taiwan, hospital performance evaluations largely focus on managerial efficiency and rarely on healthcare quality, together with the growing shortage of medical professionals, the conventional performance evaluation models can thus no longer truly reflect current situation. In this context, the authors proposed a practical hospital performance evaluation method based on the data envelopment analysis. The method comprises two stages. During the first stage, a technical efficiency evaluation model was developed to calculate the optimal managerial performance of hospitals, while in the second stage, results from the first stage were incorporated into the analysis of healthcare quality to create a comprehensive efficiency model that conformed to current situations. Hospitals evaluated in this study include medical centers, regional hospitals, and district hospital; data analyzed in this study has encompassed a large portion of the acute medical care of the entire country. The research results and findings of this study accurately match the current situations. For hospitals failing to reach ideal efficiency values, suggestions for adjusting bed configuration were proposed.