Using the coupling coordination degree model to evaluate the level of integration between science and technology and the economy, combined with social network analysis to present the collaborative relationships among innovation entities, this study systematically analyzes the current status and core pain points of the integration of science and technology and the economy in China. It constructs a “policy-market-society” triple-driven mechanism and proposes differentiated implementation paths for the eastern innovation highlands, the central and western catching-up regions, and the northeast old industrial base. The research shows that the foundation of the integration of science and technology and the economy in China is gradually solidifying, but issues such as regional imbalance, hindered factor flow, and inefficient achievement transformation are prominent. The differentiated paths can precisely address development bottlenecks in various regions and provide practical guidance for high-quality economic and social development.