Governmental R&D subsidy for the enterprises aims to encourage the innovation activities of the enterprises but different supporting methods may produce different impacts on the enterprises innovation activities. This paper divides government R&D subsidy into two types, namely cost-sharing subsidy and performance-rewarding subsidy, considers the regulation role of venture capital, and uses the data of the listed companies on the GEM from 2011 to 2015 to explore the impacts of two different kinds of subsidies on the innovation input. The results show that the cost-sharing subsidy promotes the firms’ innovation input, while the performance-rewarding subsidy has crowding-out effect on the firms’ innovation input. Further grouping studies show that the participation of venture capital strengthens the positive effect of cost-sharing subsidy on the innovation input, and it weakens the crowding-out effect of performance-rewarding subsidy on the innovation input. Governments should boost cost-sharing R&D subsidy, R&D type enterprises should actively bring in venture capital so as to promote innovative input growth.