Spatial economic structure is the relationship and distribution forms of economic elements in certain geographical area, it is a form of economic activity in areas, it reflects the regional characteristics of the economic activity and the relationship between geographical areas. In this paper, Exploratory Spatial Data Analysis(ESDA) is adopted to analyze the spatial economic structure since Chongqing became municipality (1997-2011), the objective includes 15 cities, suck as Chengdu, Guang’an and other 31 counties, such as Yuzhong District of Chongqing, Wanzhou District etc, to reveal the characteristics of spatial pattern of Chengdu-Chongqing Economic Zone and evolutionary process of spatial pattern,and to provide the supporting of the establishment of Chengdu-Chongqing Economic Zone regional planning for decision making. The results show there are serious deficiency in spatial economic structure of Chengdu-Chongqing Economic Zone,optimizing the spatial economic structure and strengthening the coordinated development of regional have a long way to go.