This study applies 3-stage data envelopment (DEA) of 24 listed companies in the development zone of Hubei Province from 2012 to 2017 based on the panel data; we used the DEA-Tobit model and regression analysis method on the sample in order to measure the factors affecting the innovation efficiency of listed companies and the efficiency of corporate innovation. The results demonstrated that the innovation efficiency of listed companies in the development zone of Hubei Province is relatively low. It is necessary to improve the innovation system of the development zone and give the full initiative to the role of corporate innovation as a mainstay. The four environmental variables of the number of enterprises, government subsidies, foreign direct investment in the development zone, and fixed asset investment have a significant impact on innovation efficiency. The enterprise size, operating capacity, and state-owned shares of the company have a significant positive impact on the innovation efficiency. But the number of years of the establishment has a significant negative impact on innovation efficiency. Moreover, the quality of the workers is not significant. Therefore, we must increase government investment in innovation to expand the scale of listed companies in the development zone, improve the environment for foreign investment, further strengthen the construction of talented people of companies, and enhance the original ability of innovation.