Although corporate capability has been recognized as a key factor affecting corporate acquisition performance, the role of R&D capability in acquisition performance has not been fully explained. The aim of this paper was to research the impact of internal R&D on acquisition performance according to a sample of 215 acquisitions of Chinese listed pharmaceutical companies from 2012 to 2016. First, it was found that R&D has a significant negative effect on acquisition performance. Furthermore, it was confirmed that the acquisition motive and the ownership of the acquiring firm have a moderating effect on the relationship between R&D and acquisition performance. Compared to non-technical acquisitions, the negative effect of internal R&D on acquisition performance was reduced for technical acquisitions. Compared with non-state-owned-enterprise acquisition, the negative effect of internal R&D on the acquisition performance of state-owned enterprises was weakened. Our study enriches the research of the path dependence theory on the acquisition performance of enterprises and also the interpretation of acquisition performance on the basis of internal and external innovation and the institutional theory.