Abstract: The innovation resources misallocation is an important reason for the low efficiency of China's overall innovation. Structural misallocation is an important aspect. Through constructing a model to calculate resources misallocation degree between departments, using the industrial data from 2005 to 2015, this paper finds that: the innovation resources misallocation degree between regions is most serious, which leads to innovation efficiency loss of 17.4%. Inputs in the northeast and northwest regions is excessivet, while insufficient in the southeast and southwest regions. Misallocation between ownerships is the second, which leads to innovation efficiency loss of 6.56%. Inputs of the state sector is excessive seriously relative to the non-state sector. The last is misallocation between the high and non-high technology industry, which leads to innovation efficiency loss of 0.53%. Inputs in the high technology industry is still relatively insufficient, specially in the medical equipment manufacturing industry. The further analysis finds that the three types of structural misallocation all are mainly reflected in R&D funding compared to R&D labor.