As the core direction of the third revolution in life sciences, the industrialization of synthetic biotechnology highly relies on the integration of scientific and technological innovation and industrial innovation. Driven by both national strategic layout and technological iteration, the scale of China’s synthetic biology industry has continued to expand. However, problems such as “full-chain fragmentation” and “insufficient multi-agent collaboration” in integration of science and production have constrained industrialization efficiency. Based on the theory of science industry integration, the Triple Helix Model, and the theory of industrial ecosystems, this study constructs a four dimensional analytical framework of “technology-agent-scenario-institution” .Multi-case empirical research is conducted in four typical regions: Shenzhen, Tianjin, Changzhou, and Hefei. The research finds that the four regions have formed differentiated science-industry integration models, with core differences reflected in integration carriers, power sources, and collaborative mechanisms. Common bottlenecks include weak technological engineering capabilities, loose collaborative networks among agents, lack of high-value scenarios, and insufficient adaptability of institutional supply. Accordingly, this study proposes a path for industrial ecosystem construction: “technological breakthroughs-multi-agent collaboration-scenario empowerment-institutional innovation,” providing theoretical support and practical reference for promoting the integration of synthetic biology science and industry in various regions.