From the perspective of innovation mode differences, this paper uses the manufacturing data of 30 provinces in China from 2007 to 2014 to build a dynamic panel model, and examines the relationship between financial structure and innovation. The findings are: 1) Different risk-return characteristics of the technological innovation mode will generate a differentiated financial structure. 2) The banking system has a significant role in the promotion of imitation innovation with low risk, predictability and stable returns, and this promotion is free from market constraints. 3) Under a good market condition, the stronger the market orientation in the financial structure is, the more favorable it is to promote independent innovation with higher risk, unpredictability and uncertain returns. Therefore, in order to realize the smooth transition of China’s manufacturing innovation mode from imported imitation to independent innovation, it is necessary to promote timely transformation of the financial structure and to create a market environment conducive to the development of the financial market.