Abstract: Based on the DEA-Tobit two stage model, the innovation efficiency of China's state-owned enterprises and its influencing factors are studied. The study shows:state-owned high tech enterprises have the advantage of innovation efficiency; innovation efficiency of high-tech enterprise from different regions, or different industries is different; the government subsidies and enterprise scale is not conducive to improving innovation efficiency of the state-owned high-tech enterprises, but the export delivery value and technical transformation expenses is favorable for promoting it.