Innovation system is the innovation engine of high quality economic development in Beijing. This paper analyzes the current situation of innovation system construction in Beijing from three aspects：the main position of enterprise innovation，the construction of market-oriented mechanism of technological innovation supported by science and technology service industry，and the strategic layout of “three cities and one district” as the main platform. Then it puts forward countermeasures and suggestions to further strengthen the construction of innovation system in Beijing from the aspects of deep integration and docking of innovation chain and industrial chain，improving the innovation ability and innovation subject status of enterprises.