Abstract:The 124 prefecture level cities, autonomous prefectures and 2 municipalities of the Yangtze River Economic Belt as the research unit. The patent licensing is indicated as innovation output. Using standard deviation, coefficient of variation, ESDA, Spatial Econometric Model and other methods to study the spatial and temporal evolution characteristics, and formation mechanism of innovation output in the Yangtze River Economic Belt from 1986 to 2014.The results show that: (1) The absolute difference of innovation output in the Yangtze River Economic Belt increased slowly before 2001, and then quickly pulled up, from 256.45 in 2002 increased to 12323.68 in 2012, subsequently, significantly decreased. The relative difference generally decreased before 1994, then increased slowly, increased significantly after 2002, reached the highest point of 3.12 in 2003, the relative difference decreased obviously in 2009. Accession to the World Trade Organization in 2001 and industrial transfer after the financial crisis in 2008 has an important influence on the innovation output of the Yangtze River Economic Belt difference. (2) The number of high Innovation output cities is little change in the Yangtze River Economic Belt, distribution is more concentrated, but there is a tendency to spread to the central region, mainly located in the Yangtze River Delta region and the central and western provincial capital city of Chongqing, Chengdu, Changsha, Hefei. Over the past five years, the innovation output was improved significantly in which Wuhu, MaAnshan, Hefei, Lianyungang city. (3) The spatial correlation of innovation output in the Yangtze River Economic Belt is mainly related to main, the characteristics of spatial agglomeration are obvious, and the spatial pattern is roughly stable. Yangtze River Delta region has been the innovation output dense aggregations of the area, and in the central and western regions are mostly low concentration area and level of agglomeration, the unit is mainly the Midwest capital city. (4) Spatial interaction is an important cause of spatial difference of innovation output in the Yangtze River Economic Belt, investment in science and technology policy has a significant impact on innovation output in the Yangtze River Economic Belt. Economic development, human resources, FDI and communications infrastructure have a great impact on innovation output, traditional infrastructure to minimize the role of innovation output, And the degree of foreign investment in the regional economy has an inhibitory effect on innovation output. The penetration of foreign investment in the regional economy has an inhibitory effect on innovation output.