Complex adaptation systems are the main development direction of China’s current green innovation research. New material industry is one of the key entry points to accelerate the construction of modern industrial system and promote innovation, green, and efficient development. Under the requirements of China’s current low-carbon development, China’s green innovation system is developing rapidly. Green innovation complicates traditional innovation models and their functions and improves economic development. The purpose of this paper is to study the theoretical analysis framework of applying (...) complex adaptive systems and to analyze and calculate the characteristics of the current status of green innovation systems in multiple industries in China’s manufacturing industry. Analysis is as follows. The experimental group and the control group are set for comparison, and the data are organized by applying complex adaptive system theory and data analysis methods. Experimental data show that the coordinated development of the green innovation systems in various industries in China is not balanced, with a difference of more than three times; the parameters of the various green innovation systems within the industry are unbalanced, and the difference is more than five times. The experimental results show that the green innovation subject can strategically interact by adjusting the ratio of resource allocation through the constructed green innovation system model. The green innovation system with complex adaptive system theory is conducive to the development of the green system. It can save about 23% of green innovation time and improve efficiency by about 15%, to promote the development of green innovation in China. (shrink)