This study examines the empirical relation between corporate ownership structure and innovation (proxied by R&D expenditure and patent granted). Specifically, we examine two primary effects of ownership concentration: the incentive alignment effect, proxied by the controlling shareholder’s cash flow rights, and the entrenchment effect, proxied by the divergence between control rights and cash flow rights of the controlling shareholder. Based on a sample of Taiwanese publicly listed firms, we find that the incentive alignment effect positively affects innovation investments and the entrenchment effect affects innovation investment negatively. In addition, we find that the incentive alignment effect (entrenchment effect) reduce (increase) the sensitivity of the timing of R&D expenditures to sales, which suggests that the ownership structure of the controlling shareholder have important implications for myopia R&D investment behavior. Our finding shed light on the role of the controlling shareholder on corporate investment policy.