After the principle of ’Protect together and avoid exploitation’ is confirmed in Yangtze River economic zone,the economic zone’s development mainly depends on its overall planning, which is the new creative overall planning mechanism to break the administrative division and gradually lead to the joint development in the economic zone. The idea is to start from the top design and discover a way to build the governance pattern in Yangtze River. There are mainly four parts in the overall planning:interprovincial negotiation,judicial cooperation,environment supervision,and shipping system construction. This four parts present the characteristics of national overall planning and the new decentralization. Regions Inhabited by Ethnic Minority Groups have made active responses to the policy adjustments in time,which mainly include taking full advantage of the interprovincial negotiation to build the system of overall compensatory mechanism in ecological function areas,using the Webber structure to re-cooperate spatial layout in cities,immediately revising relative laws and regulations to connect with the national overall planning,and cultivating regional hub economic.