To deepen financial reform, China’s financial policy displays more regional characteristics and the expansion of financial innovation to the regions has a far-reaching impact. This paper aims to evaluate the performance of financial innovation in 30 provinces in China. By using the panel data of 30 provinces in China, we apply the three-stage data envelopment analysis (Three-stage DEA) to regional financial innovation with environmental constraints taken into account. The application of Three-stage DEA that involves environmental factors and statistical noise enables us to assess the innovation disparity in the financial industry of each province in terms of technology. The conclusions are as follows: (1) Technical efficiency and scale efficiency are significantly reduced except for pure technical efficiency in the intermediary-oriented model compared with that before adjustment. The main reason for the decrease in overall efficiency is that the real level of financial innovation declined after the external environmental factors have been excluded. And the overall level in the market-oriented model is lower than that in the intermediary-oriented model. (2) External environment variables, including the regional economic basis, government loan intervention, the founding of the regional financial market, will affect the input of regional financial industry in accounting technical efficiency. Firstly, with a higher level of economic development, the quantity of personnel employed in the financial industry tends to rise. Secondly, the intervention from the local government is positive in the slack model of capital investment input, indicating that more government intervention in one area will lead to the inefficient use of capital investment in the financial industry. The estimated value of personnel input is negative, implying that personnel redundancy is negatively correlated with government intervention. Finally, the effect of the regional dummy variable is significantly negative in the slack of capital input, indicating that the regional financial market can improve the efficiency of capital investment in the financial sector. (3) The efficiency gap between provinces and districts still exists. It is revealed in our finding that there are efficiency disparities between coastal and interior regions, and between eight economic zones as well. It is suggested that fostering a good external environment is beneficial not only to promoting the efficiency of regional financial innovation, but also to bridging the gap between developed and developing provinces. Expanding the perspective of financial innovation research, this paper extends efficiency evaluation from traditional manufacturing to financial industry. Specifically, in this paper, regional financial innovation refers to the ability to reduce costs and increase the efficiency of input factors in financial industry. However, there is still plenty of room for research in this field, such as the characteristics of financial innovation in organizational structure, the external environment of financial competition and cooperation, and the growth effect of financial innovation. These are the directions for further research.