Institutional innovation is fundamental to promoting the coordinated development of urban agglomeration and protection. At present，the development of central urban agglomeration faces a number of obstacles promoting the coordinated development of central urban agglomeration in the new period，we should actively strengthen institutional innovation and institutional designation，focus on carrying out trans-administrative pilot and establishment of strategic cooperation to organize and coordinate system，improve the modern market system，and promote the reform of financial management system，the establishment of shared systems and public service efforts. At the same time，we should plan positive reinforcement，strengthen policy support，promote reform，innovation and evaluation system and perfect the rule of law.