Based on the heterogeneity of R&D perspective, this paper divides into the R&D investment exploratory innovation investment and conventional type innovation. This paper selects 149 domestic pharmaceutical manufacturing listed companies during 2007-2013, study the effect of diversification strategy on the enterprise innovation investment model. The empirical results show that the specific operation of the pharmaceutical enterprise attaches great importance to the research stages of R&D expenditure, to explore innovation investment (R > 0, D = 0; R > 0, D > 0); Diversification of pharmaceutical enterprise preference conventional type innovation investment (R = 0, D > 0), are reluctant to put too much money into the high risk and long return cycle research stage. In this paper, the research results can be decision-making reference for pharmaceutical company executives to choose innovation investment model, and for the government financial support policy for enterprise innovation.