The economic growth of Inner Mongolia has ranked first for several years since Western Development. In this paper, we establish a level indicator system for evaluating the level of Regional Economic Development from the following four aspects: economic scale, economic benefit, economic structure and quality of life. Then, we take the data of 2000 as sample data, and apply it to a DEA model based on panel data for evaluating the economic development of the twelve union cities from 2000 to 2009.By the analysis, Inner Mongolia's economic development can be divided into two levels: Erdos , Baotou, Hohhot, Alashan League and Wuhai have a higher level of economic development, Xilinguole League, Hulunbeier, Bayannaoer, Wulanchabu, Chifeng, Tongliao and Xingan League have a poor foundation , the overall development is not ideal.