R&D investment of corporation is basis of innovation, while it is up to the decisions made by entrepreneurs, in which entrepreneurship is a key factor of making decisions. To realize “Mass entrepreneurship and innovation”, figuring out what influences independent innovation and how to strength these factors is the problem needed to be solved. This paper is based on Chinese Listed Companies 'Evidence from 2005 to 2009, and used principal components analysis to quantify the three parts of entrepreneurship: the ability of operation, startup and innovation. Then this paper discussed the relationship of entrepreneurship and R&D investment by empirical research. The study found that the ability of operation will increase the R&D investment, while the ability of startup and innovation will decrease it. What’s more, Intellectual property protection will restrain entrepreneurship in some extent, but financial development will enlarge the influence of entrepreneurship on R&D investment. And the difference of ownership property also has an impact on it. This paper analyzed the driving factors of R&D investment from the perspective of entrepreneurship, and give new empirical evidence on study on industrial upgrading and independent innovation.