<p>Seepage complications in fractured rock masses represent a significant concern in hydraulic engineering. This paper aims to investigate non-steady seepage behavior and determine the causes of excessive seepage rates in fractured rock masses containing complex seepage control systems in the Ludila hydropower station dam foundation. To achieve this goal, a novel analysis framework for seepage field in fractured rock masses with sophisticated seepage control systems was proposed. The seepage analysis framework was established by incorporating methods for determining permeability tensor, employing parabolic variational inequality approach which transforms the seepage problem within wet region into a boundary value problem for a fixed area, and utilizing drainage substructure technique. The numerical results closely agreed with empirical observations, which demonstrated effectiveness and suitability for seepage analysis in fractured rock masses with complex seepage control systems of the proposed framework. On this basis, transient seepage behavior and the factors contributing to the excessive seepage rates in the Ludila hydropower station dam foundation were investigated by combination of parametric numerical analysis and measured results. The results indicate that the grouting curtain is the main measure to control the seepage rate. A defective upstream curtain below a 60&#xa0;m depth emerges as the primary cause for excessive seepage rates on the left bank of the Ludila hydropower station dam foundation. It is crucial to ensure construction quality and integrity of the grouting curtain, especially the bottom grouting curtain, in actual engineering.</p>