Taking the demands of the national territory development and protection in the new era as the strategic goal, taking scientific and manipuility as the basic principles, focusing on solving the typical problems of the existing institution system, this study systematically reviewed the development history of the key institutions, clarified the relationship between the typical problems and their influencing factors of the key institutions, summarized the typical needs of the national  territory development and protection regulation in the new era, proposed the Spatial Planning and the territorial space use control as the strategic key point of institution system integration, and  the implementation path of the two institution system integration was analyzed from four aspects: object integration, subject integration, content and means integration.