Abstract:decomposing Innovation value chain as knowledge creation, technology absorption and achievements transformation stage, combining with the difference of industry heterogeneity and value chain, using three stage DEA modified by SFA, the three innovation value chain innovation efficiency of 17 high technology industry sub sectors are evaluated. The innovation efficiency in the technological absorption stage is low while in the knowledge creation stage and achievement transformation stage the innovation efficiency are more easily affected by environment and inflated. Technical factors play a leading role and the scale can be further expanded in innovative activities. The overall efficiency, pure technical efficiency, scale efficiency in the technological absorption stage are higher than in the stage of knowledge creation and the stage of achievement transformation which shows Chinese high-tech industry’s innovation absorptive capacity has been greatly improved while the results of knowledge creation and innovation commercialization are overall low. Investment factors of high tech industry innovation between industries exist imbalance as well as a structural imbalance in the innovation activities process.