Abstract: The hydraulic properties of compacted clay are critical to the anti-seepage performance of the core wall in earth-rock dams and are key to ensuring its seepage safety and long-term stability. A thorough understanding of the pore structure characteristics of compacted clay helps to reveal the intrinsic mechanism governing the evolution of its hydraulic properties with compaction degree. To investigate the evolution of the microscopic pore structure and hydraulic properties of compacted clay under varying compaction degrees and to clarify the relationship between them, hydraulic properties—including saturated permeability, water retention capacity, and unsaturated permeability—were obtained through permeability tests and pressure plate tests. Three-dimensional pore structures were acquired via CT scanning, and a pore network model was established to systematically analyze the evolution of pore structure characteristics and hydraulic properties, as well as their interrelationship. The results show that: (1) With increasing compaction degree, the microstructure of soil samples transitions from a loose overhead structure to a compact lamellar stacking structure. This transition blurs the boundaries between soil particles, makes the compacted mosaic structure increasingly pronounced, and gradually shifts the interparticle contact from point contact to surface contact. During this process, the number of macropores in the soil samples significantly decreases, the connected areas between pores begin to shrink, and connectivity deteriorates. Specifically, the number and radius of pores and pore throats decrease substantially, while fractal dimension and pore tortuosity increase, and connected porosity and coordination number decrease. (2) Changes in pore structure are the primary cause of alterations in the hydraulic properties of compacted clay. With increased compaction degree, the topological relationship of the pore network changes markedly. The three-dimensional pore structure contracts, and pore-throat channels around pores close or deteriorate, leading to weakened connectivity between pores. Consequently, a more tortuous and complex pore network with lower connectivity forms within the soil sample. This results in an exponential decrease in saturated permeability, an increase in air-entry value, enhanced water retention capacity, and a substantial reduction in the unsaturated permeability coefficient, indicating improved hydraulic stability. (3) At lower compaction degrees, water seepage velocity is generally higher. High-velocity seepage paths correspond to well-developed macropore pathways within the soil sample, where streamlines are relatively straight and smooth, while low-velocity dispersion paths are less prevalent. High compaction suppresses the development of seepage channels within the soil sample, causing streamlines to change from relatively straight and smooth to dispersed and complex, with a significant reduction in flow velocity. (4) According to grey correlation analysis, the correlation degrees between different microscopic pore parameters and hydraulic parameters vary considerably. The average pore radius has the greatest influence on the saturated permeability of clay, showing a strong correlation with it. The fractal dimension reflecting pore complexity exhibits a significant correlation with the parameters n and m, playing a dominant role in the evolution trend of the soil-water characteristic curve. Residual volumetric water content and air-entry value show the strongest correlation with tortuosity and the weakest correlation with average pore radius. These findings help to understand the differential response of the hydraulic properties of compacted clay to compaction degree and its underlying mechanisms, thereby providing important engineering and theoretical references for the disaster prevention and mitigation of clay core-wall dams. In future studies, the effects of wetting-drying cycles on the microstructure and hydraulic properties of compacted clay warrant further investigation. Moreover, in research related to the hydraulic and mechanical behavior of rock and soil, as well as in geology and water conservancy engineering, a deeper understanding of mechanisms can be achieved by integrating micro- and meso-scale analyses with advanced testing techniques and analytical methods. Such an integrated approach helps to elucidate macroscopic test phenomena and evolutionary laws, thereby providing theoretical guidance for the prevention and control of engineering problems and the optimization of engineering materials.