Based upon the reality condition of the economic development and discipline structure of higher education of Chongqing, 11 indicators are selected, which reflect the discipline structure of higher education, and 9 integrated indicators are selected, which reflect the economic development Then, the paper analyzes the relatedness and builds the relation model between economic development and discipline structure of higher education of Chongqing from 1999 to 2006 by using quantitative analysis, such as multiple regression analysis and principal component analysis The results show that discipline structure of higher education is basically in harmony with economic development of Chongqing, and some adjustment is necessary according to the relatedness It provides some reference pathes for discipline structure adjustment of higher education of Chongqing