My country’s current research on the influencing factors of total factor productivity has problems such as single evaluation method, low efficiency, and poor overall level in terms of evaluation methods and evaluation efficiency. Based on this, this study divides the financial structure into three traditional sections, banking, securities, and insurance, and uses the DEA model to study the temporal and spatial differences of the financial structure’s influence on the total factor productivity of the four major political and economic regions of China’s eastern, western, central, and northeastern China. First, establish a DEA model based on data mining algorithms, combine financial data comparisons over the years, to achieve a quantitative analysis of the financial structure’s impact on China’s total factor productivity, calculate financial efficiency, and then combine the DEA analysis data model with the grey correlation method. Analyze its internal influence rules, and design experiments for model verification analysis. The results show that the DEA analysis model can realize 8 iterations of data on the impact of financial structure on China’s total factor productivity, and its evaluation accuracy can reach more than 96.2%.