Government officials, motivated by promotion, have unreasonably pursued the increase in the number of patents. As a result, innovation subjects only pay attention to the increase in the number of patents, ignoring the improvement of patent quality, and thus affecting economic growth. Based on the conflict between administrative incentive and market choice, the deep causes of the malformation of patent structure in China at the theoretical level were analyzed, and the fixed effect model was used for empirical analysis to verify it. It can be concluded that the crude quantitative assessment system leads to inefficient allocation of scientific and technological research resources, and a new assessment system based on quality and quantity must be established in order to completely change the deformed patent structure.