The article analysis the green innovation efficiency about high-tech industries by Super-SBM model with China’s High-tech panel data between 2006 and 2012, study on R&D investment Intensity how to impact on the green innovation efficiency about high-tech industries by the nonlinear threshold model. The research show that: measure the innovation efficiency using Super-SBM model is more actual, the eight zone’s green innovation efficiency exist great differences. The double threshold effects of the R&D investment Intensity on green innovation efficiency with the enterprise scale as the threshold variable, Government behavior, market environment, Industrial assemble have significant positive effect with the innovation efficiency while human capital have not play obvious effect.