Based on the panel data of Fast & Furious 9 City in the Pearl River Delta from 2004 to 2016, this paper analyzes the influence mechanism of real estate investment on scientific and technological innovation, and uses the intermediary effect model to identify and compare the deep‐seated conduction effect. The study finds that the impact of real estate investment on different types of innovation activities has regional homogeneity and heterogeneity. In economically developed areas, real estate investment has a restraining effect on all types of scientific and technological innovation activities, while in economically underdeveloped areas, real estate investment has a promoting effect on the innovation of medium and low‐end types. In addition, there is regional heterogeneity in the transmission mechanism. There is no intermediary effect in the economically developed areas, but the intermediary effect is significant in the economically underdeveloped areas. And within the transmission mechanism, there is also heterogeneity in the types of innovation activities. Therefore, when the local government formulates relevant policies, it needs to adjust measures to local conditions, not regard the real estate industry as a problem in economic development, but should grasp the balance of economic development and make rational use of the capital advantages of real estate investment.