This study investigated the efficiency performance of the production technology of the Department of Health (DOH)-affiliated hospital system in Taiwan in different competitive environments. This study used Data Envelopment Analysis (DEA) to analyze a total of 396 hospitals of different systems in Taiwan. The results indicated that, in terms of the internal competitive environment, the production performance of hospital Q was the best, while that of hospital N was the worst. This study also analyzed the production performance and scale of DOH-affiliated hospitals and provided hospitals with a direction for scale development. Finally, this study proposed suggestions on improvement direction for hospitals with poor production performance. As for external competitive environment, there is no significant difference in the average efficiency among various hospital systems. However, there are a lot to be improved in DOH-affiliated hospitals, especially in the aspect of technology efficiency. The improvement of technology efficiency should be more beneficial to the overall efficiency.