Due to the urgency of industrial agglomeration transformation and the inherent advantages of industrial clusters, the pilot projects of innovative industrial clusters are carried out in high-tech industrial parks. Innovative industrial clusters have become an important way for national high-tech zones to promote strategic emerging industries. This paper takes the construction of innovative industrial clusters as the quasi-natural experiment, and uses the double difference method to evaluate the effect of innovative industrial clusters on the innovation efficiency of high-tech zones. The conclusions show that compared with the control group, the construction of innovative industrial clusters significantly improves the innovation efficiency of the experimental group; compared with the eastern and northeastern regions, the innovative industrial clusters have a more significant impact on the innovation efficiency of the central and western regions. The western region will expand the scope of policy implementation and overall enhance regional industrial innovation capabilities.