Under the new development pattern of domestic and international dual circulation, building a unified national market is the core strategy to stimulate endogenous economic power. Based on urban panel data from 2015 to 2023, this study takes the construction of national strategic emerging industry clusters as a quasi natural experiment and uses a difference in differences model to explore the impact of cluster construction on regional market integration. Research has found that the construction of strategic emerging industry clusters promotes regional market integration, and this conclusion still holds true after robustness testing. Mechanism analysis shows that cluster construction mainly promotes market integration through two paths: optimizing factor allocation efficiency and weakening local protectionism. There is a clear differentiation in policy effects: cities with multiple clusters and well-developed transportation infrastructure have more prominent market integration effects. In addition, cluster construction has a positive spillover effect on market integration in neighboring cities, and the indirect impact is better than the local direct impact. The research provides theoretical and empirical evidence for the joint promotion of strategic emerging industry clusters and the unified national market.