As the number of “ownerless” enterprises in China’s capital market increases, so does the importance of paying attention to their behavior. From the perspective of enterprises’ control rights allocation, we find that non-actual controllers can inhibit corporate innovation by intensifying agency conflicts, reducing corporate risk-taking and strengthening financing constraints. We also find that a larger proportion of independent directors, higher audit quality, greater managerial ownership and less environmental uncertainty weaken the negative effect of non-actual controllers on corporate innovation. In contrast, multiple large shareholders strengthen the inhibitory effect of non-actual controllers on corporate innovation, but this inhibitory effect comes from over-supervision rather than from collusion. We further divide non-actual controllers into real and hidden types and find that real non-actual controllers still have a significant inhibitory effect on corporate innovation. Finally, we rule out the competitive explanation of equity dispersion, whereby non-actual controllers inhibit corporate innovation. This study enriches the literature on the factors influencing corporate innovation and provides evidence of the adverse impact of non-actual controllers.