This paper uses SFA to empirically measure the innovation efficiency of military listed companies from 2009 to 2016, and discusses the impact of defense technology financing methods on its innovation efficiency. The results show that the efficiency of Chinas national defense science and technology innovation has been improved year by year, but the increase rate is slow. R&D expenses and R&D technology personnel have a significant positive impact on innovation efficiency, and there are big differences in innovation efficiency between different industries. Endogenous financing, bond financing and government subsidies have a significant role in promoting the efficiency of national defense science and technology innovation. Equity financing has a certain negative impact, and the impact of bank loans is not significant. Diversified financing methods can enhance the innovation efficiency of invention patents and utility model patents as output variables, and the expansion of financing channels will inhibit the innovation efficiency of design as output variables. Through the interaction test, it reveals that profitability and industry monopoly will have an impact on the relationship between financing methods and national defense technology innovation efficiency.