Taking Chinese high-tech industries as samples, this paper empirically examines the relationship among government R&D subsidies, property rights and innovation performance. The results show that the high intensity of subsidies could significantly reduce the innovation incentive effect of government R&D subsidies. The growth of private economy could significantly improve the positive effect of government R&D subsidies on innovation performance. Further analysis shows that the overall intensity of government R&D subsidy in 2005, 2011 and 2013 is high; after 2007, the proportion of private economy has been in a reasonable range. In terms of regions, there are as many as 12 provinces with excessive subsidy intensity, and most of them are in the central and western regions.The proportion of private economy is too low in 7 provinces, and most of them are in the western regions. 14 provinces including Beijing, Tianjin and Hebei are within the reasonable range in terms of subsidy intensity and private economy, while 5 provinces including Shanxi, Jiangxi and Hubei are within the unreasonable range in terms of both subsidy intensity and private economy. Therefore, setting a reasonable amount of subsidies and giving full play to the advantages of the private economy is the key to truly play the role of government R&D subsidies and realize the innovation and development of high-tech industries.