M&A is a popular strategy for pharmaceutical industry due to high R&D risk and costs. Prior research related to post-M&A performance mainly focused on the financial and technology resource perspectives. This study aims to provide a new perspective of innovation strategy which is inspired by the research of March (1991), who noted the difference between exploration and exploitation. Moreover, we build the bridge between M&A and innovation strategy by applying the resource-based view theory. We argue that the acquirer’s exploration strategy will negatively influence the post-M&A innovation performance and the innovation strategy similarity between the acquirer and the target is beneficial for future innovation. Furthermore, we hypothesize that there is a negatively moderating effect caused by the acquirer’s exploration strategy on the effect of innovation strategy similarity. On the basis of 89 M&A deals in the pharmaceutical industry, our empirical results suggest two important findings. First, post- M&A innovation performance is influenced by acquirer’s innovation strategy, more specifically, acquirer’s exploration is harmful for post-M&A innovation. Second, the similarity effect is moderated by acquirer’s innovation strategy. Precisely, acquirer’s exploration will diminish the positive effect of similarity.