Abstract: The implementation of the national innovation-driven development strategy need to fully know about the level of investment in technological innovation, and the R&D capital stock is one of the most important components. Based on the characteristics of R&D activities, this paper resets the lag period, the depreciation rate, R&D expenditures price index and the base-year capital stock, and then re-estimates the regional R&D capital stock of 31 provinces in China during 1998 and 2012 by using the Perpetual Inventory Method. Meanwhile, this paper also measures the regional disparity of R&D capital stock through the Theil index. The results show that most of the regional R&D capital stock reveals a trend of growth, but the increase of the growth rate has slowed after 2001, and the disparity of R&D capital stock is shifting from mainly intra-regional-oriented difference to mainly inter-regional-oriented difference. What’s more, the integrate disparity and inter-regional disparity take on a V-typical evolutionary track, while the disparities between different regions are diminishing and become stable.