The development of military-civilian dual-use high-tech and joint technological innovation is important for military-civilian integration enterprises to develop in-depth military-civilian integration. Taking 10 military-civilian listed enterprises in Jiangsu Province as the research objects, and using DEA-BBC model and DEA-Malmquist index method, this paper constructs an evaluation system for technological innovation performance of enterprises, evaluates and studies the innovation performance from 2016 to 2019. The research shows that the technological innovation performance of enterprises is generally low. The main reasons of this situation are backward technology, low resource utilization, and the uneven management capabilities of enterprises. In addition, this paper provides some suggestions for improving the technological innovation performance of military-civilian enterprises.