Abstract: This article utilizes the index of factor market distortion and the inter-provincial panel data of China’s high-tech industries during the period of 1997 to 2009 to make an empirical study of factors market distortions influence on the R&D input. The results show that factor market distortion has significantly different effects on R&D capital investment and R&D manpower input. It has an negetive impact on the R&D capital investment, but promotes R&D manpower input. Moreover, After the WTO, the negetive impact on the R&D capital investment declines, the impact on R&D manpower input changes to be insignificant. There are regional differences of factors market distortions influence on the R&D input, and enterprise features play an important role. In the enterprise of larger scale, or higher openness, or high capital intensive, the negetive impact on the R&D input is smaller. In addition, new product demands, financing environment, financial investment and intellectual property protection are all important environmental factors which affect R&D input.