The "Double First-class" disciplines are not only related to the development strategy of the national colleges and universities, but also to the regional science and technology innovation and development from the meso level. This paper developed from the combination of the development of "Double First-class" disciplines and regional innovation by taking Shanghai as sample city and using the " Global Innovation Center" in the construction of information technology, bio medicine, equipment manufacturing and the related areas in national "Double First-class" strategy. Taking Web of Science database as the data source and 2012-2016 as the time window, this study studies the trend analysis of output level, discipline superiority, and enterprise collaboration innovation structure, and forms a comprehensive analysis of development level in "Double First-class" disciplines in key industrial areas of Shanghai. It found that the growth rate of publications and  of "Double First-class" disciplines is lower than that of overall in Shanghai, and the proportion of its enterprise collaboration also exists the promotion room. Bio medicine and equipment manufacturing all have the characteristics of "Double First-class" leading disciplines while the disciplines of information technology needs further upgrading and strengthening.