Abstract: This report, based on the theory of national innovation system, proposes an analysis framework of monitoring analysis of China's enterprise innovation. It also constructs the monitoring index system of enterprise technology innovation. It can reflect the dynamic changes of enterprise innovation through index. The result of monitoring analysis showed that during 2000 to 2012, China's enterprises have entered a rapid development period. Enterprise innovation input, especially R&D input, has formed a large scale and achieves great results. However, there are still many challenges. This report analyses the influencing factors and gives relative suggestions.