Carbon peaking and carbon neutrality are important contents of the green technology innovation system, as well as the construction of the green defense technology innovation system. The green national defense science and technology innovation system has special attributes such as urgency of progress, market orientation, dual orientation, and the complexity of the control mechanism. It is necessary to adhere to the market orientation to promote the construction of the green national defense science and technology innovation system. Emphasizing the market-oriented green defense science and technology innovation system, the internal mechanism is to optimize the efficiency of enterprises' green defense science and technology innovation activities with the help of the market's supply and demand mechanism, competition mechanism and price mechanism. Three dimensions of industry and green finance should be considered to promote the "seamless connection and organic integration" of innovation chain, industrial chain and capital chain. To build an efficient green defense science and technology innovation system, it is necessary to overcome restrictive factors, strengthen green innovation ideological guidance and goal guidance, establish a green technology supply system that meets market demand, promote the transformation of green defense science and technology innovation achievements, strengthen the protection of green defense intellectual property rights, and create a good environment for green defense technology innovation environment.