To address the long-standing disconnect between science and technology and the economy in China, there is an urgent need to promote the deep integration of the innovation chain and the industrial chain. However, the existing research on the integration of these two chains has not yet formed a systematic theoretical framework, and there is insufficient exploration of the connotation, extension, underlying logic, and influencing factors of their integration. This study, based on the clarification and definition of the concept of integration between the innovation chain and the industrial chain, attempts to construct an analytical framework for their integration and validates it through the analysis of China’s experiences in this regard. Firstly, from the perspectives of the innovation process and system, the study defines the integration of the innovation chain and the industrial chain as a coordinated three-dimensional approach—encompassing elements, entities, and institutions—linking the entire process of “science, technology, market and industry”. Secondly, based on the “knowledge production, knowledge diffusion, knowledge application” process and the “elements, entities, institutions” framework, the study constructs an identification framework for the influencing factors of innovation chain and industrial chain integration. Furthermore, grounded in the reality of China’s technological innovation and industrial development, and using the established identification framework, the study identifies issues in China’s integration process, such as insufficient capacity for original innovation, inadequate depth of university-industry-research cooperation, and weak transformation of scientific and technological achievements. The study then proposes optimization paths and development strategies from the perspectives of innovation chain-driven industrial chain integration and industrial chain-driven innovation chain integration, and summarizes the typical international practical experience. Finally, the study looks forward to future research on the integration of the innovation chain and the industrial chain from the angles of shifts in research paradigms, innovation policy transformation, digital transformation, and sustainable development. This study provides a systematic reference and scientific basis for the theoretical advancement and practical promotion of the integration of the innovation chain and industrial chain.