This paper bases on panel data in 2012-2015 years, studies innovation efficiency and influence factors of the silk road economic belt in China by using DEA-Tobit model based on BCC model and Malmquist index. The result shows that: innovation efficiency still have a certain gap from frontier and the low level of scale technology efficiency is the main factor restricting the enhance of efficiency；Malmquist index of innovation efficiency showed a trend of declining and technology retrogression is the main factor of restricting the enhance of total factor productivity；hardware, economic, cultural and business environment have a positive influence on innovation efficiency but market environment has a negative influence on innovation efficiency. This paper put forward some suggestions on promoting the innovation efficiency of the silk road economic belt in China bases on research conclusions.