This research examines the effect of the R&D expenditures and CEO compensation research. Considering the industry、ownership structure、financial situation between CEO compensation and R&D expenditures in difference environment. We examine a sample of Taiwan listed companies in the period of 2005~2009. We find that R&D expenditure and the CEO compensation is positive. But, R&D expenditure and the CEO compensation in High-technology industry (R&D、CEO) is positive small. In addition, the managers control the enterprise, managers are more likely to improve their pay, while reducing R & D expenditures.