Most of studies about the capital structure influencing factors from the perspective of industrial organization theory focus on the impacts of price, production, industry characteristics etc. on capital structure under the premise of firms homogeneity. Different from existing researches, this article, under the premise of firms heterogeneity, tests the relationship between different strategic assets investment characterized by specificity and capital structure using empirical research method based on the transaction cost theory. The research conclusion is that strategic assets investment is negatively related to the capital structure, and the influence degrees of different strategic assets investment on capital structure are different, which are reputation investment, technology investment, R&D investment, human capital investment and relationship investment from high to low in turn. This article has important significance for improving capital structure influencing factors’ theory research from the perspective of industrial organization and the optimization of China ChiNext companies’ capital structure.