Abstract: Using the synthetic control method (SCM), based on the "counterfactual" perspective, this paper examines and compares the effects of the first batch of national innovative industrial cluster policy implementation on regional innovation ability in 2013 with the data of 31 provinces in 2001-2016 years. Meanwhile, the effectiveness of the placebo effect method based on time and space and the method of permutation test were analyzed, and the sensitivity analysis was carried out by leave-one-out iterative method to test the robustness. The conclusion shows that the implementation of the first batch of national innovative industrial cluster policies in 2013 significantly promoted the improvement of regional innovation capability. Based on this, we further analyze and verify the mechanism of innovation based industrial clusters to promote regional innovation, namely, innovation network mechanism, government support mechanism and industrial agglomeration mechanism.