Abstract Based on the perspective of internal control weaknesses and the dimension of state-owned group, this paper takes the listed companies of state-owned group from 2009 to 2019 as samples to examine the impact of internal control material weaknesses of the listed companies of state-owned group on their R&D investment. The study finds that internal control material weaknesses can inhibit the companies’ R&D investment. The test of influence mechanism shows that the negative impact of internal control material weaknesses on the companies’ R&D investment is due to the internal control quality rather than financing constraints. And the heterogeneity test indicates that the inhibitory effect of the internal control material weaknesses on R&D investment is stronger for the state-owned companies with high level of agency cost, low degree of marketization. The conclusions not only expand the research on innovation investment of listed companies from the perspective of state-owned groups, but also provide theoretical analysis and empirical evidence for improving the innovation governance of listed companies of state-owned groups.