Theoretical studies have show that R&D investment has value relevance, and government subsidies has moderating effect on the relationship between R&D investment and corporate value. Based on data of 278 strategic emerging companies from 2010 to 2014, the paper investigates how subsidies affect R&D creating company value. Results show that R&D investment significantly reduces current financial performance and market value, while significantly improves financial performance lagged two periods and the enterprise value lagged three periods. The relationship between the lagged government subsidies and company value is significantly negative, while lagged government subsidies have additional effect of corporate financial performance .