US trade tariff sanctions against China since 2018 and the events of “ZTE” and “Huawei” have put forward in-depth thinking on the core technology innovation of manufacturing enterprises. An important reason for the lack of innovation driving force of Chinese manufacturing enterprises is that there are obvious constraints on R&D investment and financing. Different financing sources correspond to different contractual relationships and constraint mechanisms. The financing structure composed of multiple financing relationships has a profound impact on the investment decision-making of enterprises. By establishing the dynamic optimization model of corporate investment in the incomplete capital market, this paper studies the impact of corporate financing structure on innovation investment, and which financing channel can effectively alleviate the fluctuation of innovation investment. According to the study, this paper gets the following findings: First, the innovation investment level of listed manufacturing enterprises in China has not reached the optimal, and enterprises are more inclined to meet the demand of innovation investment through external financing. Second, in the inner structure of external financing, equity financing contributes the most to enterprise innovation investment, followed by government financial subsidies. Although debt financing represented by bank credit is the most important financing channel for manufacturing enterprises, it contributes the least to innovation investment. Third, equity financing fluctuations have a significant negative impact on enterprise innovation investment, internal financing and government financial subsidies play an important role in smoothing short-term innovation investment fluctuations, while debt financing and equity financing impact will form a synchronous effect, accelerating the deterioration of innovation investment of manufacturing enterprises. Therefore, the government’s policy should pay more attention to the following aspects: First, improve the external financing environment of manufacturing enterprises. Second, comprehensively establish a capital reserve system for the innovation of manufacturing enterprises. Third, refine the government’s policy to support technological innovation in manufacturing industry. As to the contribution of this paper, on the one hand, it attempts to use the analysis framework of dynamic optimization model of enterprise investment, by relaxing the original theoretical assumptions and adding external financing factors to the model to expand the existing relevant theories. On the other hand, it studies whether the diversified financing channels will form a smooth mechanism for the fluctuation of enterprises’ innovation investment under the impact of equity financing market.