Under the background of the continuous deepening of financial performance management and the continuous improvement of regional coordinated development, the financial operation efficiency of local public institutions and its economic linkage effect have attracted increasing attention. Focusing on the problem of financial operation efficiency of local public institutions and coordinated development of regional economy, this paper constructs a five-dimensional index system covering capital allocation, budget implementation, asset use, public service output and financial sustainability. It introduces feature coding, adaptive weight learning, time window input and efficiency mapping methods, and establishes a data-driven financial operation efficiency measurement model. Coupled coordination analysis and dynamic prediction method are used to identify regional coordination states. The results show that the Accuracy of the proposed model is 91.8%, the F1-score is 90.9%, the RMSE is only 0.041, and the prediction accuracy of the coupling coordination degree is 89.6%. The coupling coordination degrees of the Yangtze River Delta, the Pearl River Delta and the Beijing-Tianjin-Hebei region are 0.959, 0.954 and 0.946, respectively, and the maximum difference between different time Windows in the robustness test is not more than 0.015. The results show that there is a significant positive correlation between the financial operation efficiency of local institutions and the level of regional economic coordination, and the improvement of financial operation efficiency can provide support for the optimal allocation of financial resources and high-quality coordinated development of regions.