In this paper, we investigated the relationship between financing structure and innovation, using the strategic emerging industries of Ashare listed firms from 2010 to 2012. The main conclusions are found as follows: (1) Internal financing has a significant positive effect on innovation. (2) There is a positive correlation between equity financing and innovation. (3) Debt financing for emerging industries of strategic enterprises listed inhibit innovation. After considering firm heterogeneity, the above conclusions on the low level of financing constraints, the young and smallscale enterprises is equallyapplicable, but the high degree of financing constraints, mature and largescale innovation is mainly dependent on internal financing. Further analysis shows that, there are some differences affect the financing structure of the different nature of the business property of enterprise innovation in the strategic emerging industries. In the central and local governmentowned companies, the relationship between financialstructure and innovation is not significant; the private equity companies are mainly dependent on internal financing and equity financing, debt financing have a negative effect on innovation. This article has profound policy implications that it should be vigorously developing the equity financing market, improve the proportion of direct financing, and reduce the level of leverage.