The biotechnology industry is a development focus in Taiwan. This study uses data envelopment analysis to investigate the operating efficiency of 96 listed biotechnology firms between 2014 and 2016 and further explore the factors that influence the operating efficiency. The results reveal that 19 firms showed an operating efficiency of 1 throughout the 3 years. For the firms that did not achieve the satisfactory efficiency, this study suggests that they adequately allocate the resources to be invested to increase the operating efficiency. Furthermore, this study divides the influencing factors into two types. The first type comprises general factors. We found that the operating efficiency is influenced by both listing location and the year of establishment. The second type comprises factors related to corporate governance. However, the effects that the shareholding ratio of managers, the board chairperson concurrently serving as the general manager, the shareholding ratio of blockholders, and foreign investors’ shareholding ratio have on the firms’ operating efficiency are nonsignificant.