Implementing the intellectual property protection strategy is the core essence of shaping China’s strategic resource development advantages and enhancing its international competitiveness. The study set the period from 2008 to 2023 as the research period, selected panel data from 276 cities, and used the national intellectual property pilot demonstration city policy as a quasi natural experiment to construct a difference in differences model and a mediation effect test model. The study empirically considered the relationship between intellectual property protection strategy, intelligent innovation agglomeration, and the chain transmission mechanism between the two. The main research conclusions are as follows: The benchmark regression results show that intellectual property protection strategies can have a positive impact on intelligent innovation agglomeration, and this conclusion still holds true after model validity and robustness tests. The identification results of the mechanism of action show that the intellectual property protection strategy promotes the expansion of the technology market scale and reduces the spillover losses of non active technological innovation through two transmission paths to facilitate the agglomeration of intelligent innovation. The heterogeneity analysis results show that compared to the northwest region of the Hu Huanyong Line and areas with average innovation environment, the positive promotion effect of intellectual property protection strategy on intelligent innovation agglomeration is more significant in the southeast region of the Hu Huanyong Line and areas with excellent innovation environment.