Strategic alliance partner search breaks the constraints of the search scope and knowledge structure in the core enterprise technology development trajectory, which is the important source for core enterprises to gain the competitive advantage. Based on the innovation search theory and resource-based view, we proposed the hypothesis model about strategic alliance partner search, strategic flexibility and breakthrough innovation of core enterprise. This paper obtained the following key findings: different dimensions of strategic alliance partner search have a significantly positive impact on breakthrough innovation, strategic flexibility has a significantly positive impact on breakthrough innovation, and strategic flexibility as an intermediary variable played a mediating role in the relationship between strategic alliance partner search and breakthrough innovation.