Establishing an effective central and local coordination mechanism is of great significance to solve such problems as lack of top-level design, inconsistent industrial policies and serious homogenization of industries in the coordinated development of strategic emerging industries. Based on the difference of the role of central government and local government in promoting the development of strategic emerging industries, this paperputs forward that the central-local coordination mechanism should be constructed from three levels: government leading, enterprises participating and third party organizations assisting, including policy coordination mechanism, benefit sharing mechanism, exchange and cooperation mechanism and intermediary service mechanism.we should also strengthen the construction of policy, improve the mechanism of binding, construct information communication platform and perfecting the intermediary organization structure to ensure efficient and effective coordination mechanism.