The performance of government subsidies has been focused on by many researchers. Based on the literature review, an empirical model is set up in order to evaluate the effect of government subsidies on enterprise R&D investment by using Zhejiang private science and technology enterprises database. Then the stimulation effect is analyzed from size of enterprise, intensity of R&D, and intensity of government subsidies respectively. The main empirical discoveries are following: there is a significantly positive effect of government R&D subsidies on private R&D input of one-year lag; the bigger size of enterprise, the better effect of stimulation; the larger intensity of R&D subsidies, the better effect of stimulation; and the enterprise intensity of R&D has the effect on the performance of government R&D subsidies to private R&D investment.