Based on the agency theory and innovation theory, we analyze the effect of ownership concentration on independent innovation investment in high-tech enterprises. Taking A-share listed high-tech enterprises in China as a sample, using simultaneous-equation models and three-stage least-squares method, this papers empirically analyses the relationships among ownership concentration, managerial compensation package and independent innovation investment in enterprises of different control rights. The research results indicate that: (1) in state-owned high-tech enterprises, the higher the ownership concentration, the higher the managerial monetary compensation and the lower the equity compensation，and lower equity compensation further induces manager to raise monetary compensation; while in non-state-owned high-tech enterprises, the higher the ownership concentration, the lower the managerial monetary compensation and the higher the equity compensation，and higher equity compensation further strengthens the managerial power to raise monetary compensation. (2) In state-owned high-tech enterprises, increasing monetary compensation will induce managers to reduce the independent innovation investment, but in non-state-owned high-tech enterprise, increasing monetary compensation will encourage managers to increase the independent innovation investment; in both the state-owned and non-state-owned high-tech enterprises, the managers' equity compensation has an "N-type" impact relationship on independent innovation investment.