The transformation and upgrading of China’s CNC machine tool industry to break free from the scale economy trap is a significant issue related to the enhancement of China’s manufacturing industry’s international competitiveness. This paper focuses on the competitiveness of China’s CNC machine tool industry and explores the co-evolution of industry base capabilities and national industrial governance structures from the perspective of dynamic evolution theory and the “chain-creation coupling” mechanism. This study first analyzes the relationship between industry base capabilities and the evolution of national industrial governance structures, and then summarizes lessons from developed countries. Based on this, it proposes the mechanism of China’s CNC machine tool industry innovation chain and industry chain double-helix coupling, analyzes the evolution stages of China’s CNC machine tool industry innovation chain and industry chain double-helix coupling, and finally suggests policy target selection in stages. This paper establishes a framework for the relationship between industry chains, innovation chains, and national industrial governance structures, reimagines the highly dynamic process of double-chain integration, and constructs a double-helix coupling model from four dimensions to analyze the coupling forces in terms of pairing, integration, linkage, and attraction. The research results of this paper can be used to study how industrial innovation and incremental improvements of various elements separately affect a company’s market position, as well as how the combination of various elements affects two types of innovation. On the other hand, it can be used to explore how various elements of the two types of innovation couple to form a systemic driving force, identify the “action paths” of policy targets, and thereby establish a new governance system for China’s CNC machine tool industry.