This paper takes China’s A-share listed companies in 2006-2016 as a sample, and divides fund investors into long-term funds and short-term funds according to the average position time. It empirically analyzes the impact of funds of different transaction nature on enterprise R&D investment. The research findings in this paper are as follows: Different from the “short-sighted theory” in previous studies, short-term fund does not inhibit the investment in research and development, and long-term fund ownership can significantly promote the innovation investment of the company. In high-tech enterprises, this kind of promotion effect is inhibited, but the inhibition effect is not obvious.