Taking the state-owned high-tech enterprises which listed in China’s A-share market from 2015 to 2018 as the research object, this paper empirically tests the impact of mixed ownership reform on innovation investment of state-owned enterprises, and analyzes the role of ownership characteristics and control right allocation in the relationship between them. The empirical results of this paper show that the mixed ownership reform has a significant role in promoting the innovation investment of state-owned enterprises. The depth of mixed ownership, the degree of checks and balances of mixed ownership and the control right of non-state-owned capital all play the most important role in promoting the innovation investment of enterprises. The critical value of the degree of checks and balances of mixed ownership in the eastern region companies is 0.4636, which is also larger than that of the whole sample and non-eastern companies.