Based on the background of China’s emerging and transitional market, government subsidies to enterprises are regarded as a “helping hand” of promoting economic structural adjustment. In this paper, using China’s A-share agricultural listed companies from 2010 to 2015 as research samples, we discuss the influence of government subsidies on research and development (hereinafter referred to as R & D) investment, and the difference in the relationships between the two from the perspective of different nature of property rights. The results show that, on the whole, the increase in government subsidies does not promote the intensity of R & D investment of agricultural listed companies. And after distinguishing the nature of property rights, the results show that state-owned enterprises can get more government subsidies than private enterprises, and the increase in government subsidies boosts the increase in R & D investment in private enterprises, but there is a negative correlation between government subsidies and R & D investment of state-owned enterprises. This conclusion can broaden the research perspective of the influence factors of corporate R & D investment, and it is of practical significance to further clarify the role of government subsidies in R & D investment decisions of enterprises with different nature of property rights.