Innovative City is a brand new development concept and pattern in this knowledge economy era. Based on theories of Innovative City and the functions of government, this article compares Chongqing with other innovative cities in China, analyzes the current development of innovative city of Chongqing from FDI, research and education resources ，trademark registration and basic situation of science and technology activities of industrial enterprises. To mitigate the restrictive factors existed, suggestions to relative issues are given.