From the perspective of capital flow, the study analyses the preference and spatial difference of capital flow of high‐tech enterprises, and uses the Super‐SBM‐DEA model to analyze the capital allocation efficiency. On this basis, the influence of capital flow of financial institutions, capital market, government, and foreign capital flow on capital allocation efficiency is further analyzed. We found the influence of different channels of capital flow on the capital allocation efficiency is heterogeneous. Finally, suggestions are made to optimize capital flow and improve the capital allocation efficiency of high‐tech enterprises in different regions.