The innovation efficiency of enterprises has always been an important subject of concern. The characteristics of ownership in China are distinct, and the performance of innovation efficiency of enterprises under different kinds of ownership has been discussed. Based on the different input factors, innovation efficiency is innovatively decomposed into three categories: capital input, labor input and comprehensive input. We use the data of listed companies from 2015 to 2021 to compare the three categories of innovation efficiency of state-owned enterprises and non-state-owned enterprises. We find that in terms of labor, capital, and comprehensive input innovation efficiency, as well as labor input innovation efficiency in particular, state-owned enterprises trail below non-state-owned enterprises in all three categories. Further research shows that for high-tech industry, corporate size and industry type also have an impact on the efficiency of innovation activities. Equity and tax incentives can explain the effect of privately owned ownership on the efficiency of labor and capital innovation, respectively, the principle of which lies in how to make use of the advantages of state-owned property and how to avoid the pain points of state-owned property.