In order to study the comparative advantage of Chongqing′s manufacturing industry, by screening 15 related indicators from such three important aspects as economic creative capacity affecting the level of manufacturing industry, main business management and asset indebted capacity, this paper builds index system of comparative advantages of the manufacturing industry of all provinces and municipalities of the Yangtze River economic belt, and uses the newest data and principal component analysis to make comprehensive evaluation on the comparative advantage. The results show that Chongqing′s manufacturing industry, as a whole, is located at the fifth place in the Yangtze River economic belt and belongs to the second team as Zhejiang, Sichuan and so on. This paper measures the regional entropy in recent years in the belt, obtains the periodic regional entropy of all provinces and municipalities of the belt and Chongqing′s position, and calculates recent industrial agglomeration index of all industries of all provinces and municipalities of the belt. The research indicates that Chongqing′s six manufacturing industries such as transportation equipment, communication and electronics as well as medicine industry and so on have comparative advantage, the first two industries have significant comparative advantage. Based on this, the related countermeasures and suggestions are put forward.