Taking A-share listed companies in Shanghai and Shenzhen stock exchanges as research samples, this study discusses the impact of malposition incentives for businesses systemic issues arising from total factor productivity. The results show that the malposition of incentive mechanism inhibits the growth of total factor productivity, and this effect still exists after the robustness tests such as variable replacement and sample reset. Further mechanism tests find that the reason why incentive mechanism dislocation negatively affects total factor productivity may be that it increases agency cost and reduces R&D output. The regulation mechanism test shows that improving the quality of internal control and a certain degree of ownership concentration can alleviate the negative effects of the misalignment of incentive mechanism. In addition, the inhibitory effect of the dislocation of incentive mechanism on the improvement of total factor productivity is more significant in the period of maturity and recession.