The secondary urban agglomerations in a large city cluster can play the role of bridging the central city and the county or township, to enhance the industrial competitiveness and realize the sustainable development of the regional economy. In the context of a low carbon economy, based on the case study of a typical secondary urban agglomeration, this paper proposes that the industry chain, innovation chain, and service chain in a secondary urban agglomeration are relatively weak, which needs a complex industry collaboration system integrating industry chain, innovation chain, and service chain (IIS) to achieve low-carbon collaborative industrial development. This system can be developed by taking the real economy (industry chain) as the core and integrating innovation elements including science, technology, and knowledge (innovation chain), as well as service elements such as the material base, government policy, and financial services (service chain). The article constructs a theoretical framework for the IIS system, analyzes its operation mechanism, and finally discusses the specific construction strategy of the IIS system based on a low-carbon economy perspective.