Abstract:Firstly,through comparing the science and technology innovation base as well as innovation input and output between Shanghai and Shenzhen,the results showed that there are significant differences of the science and technology innovation between Shanghai and Shenzhen. Overall basic condition in Shanghai is better than Shenzhen,and its innovation investment is greater than Shenzhen,but science and technology innovation output in Shenzhen is higher than Shanghai significantly in terms of some important indices. Secondly,according to the conclusions mentioned above, the key causes have been analyzed,, such as differences from the innovation subject,marketization level,cultural environment,the nature of the enterprise respectively. The research shows that private enterprises of the innovation subject,a higher level of marketization,the good cultural environment is the key of the higher scientific and technological innovation achievement in Shenzhen,, comparing with Shanghai. Finally,the paper summarizes Shanghai innovative development mode characterized by the government pushing and Shenzhen innovative development mode characterized by the market driving,through comparing and analyzing the two different innovation development mode in order to provide relevant reference and beneficial enlightenment and reference for the innovation and development of other regions or urban areas.