Freeze-thaw (FT) cycles significantly affect soil permeability and could cause geological and environmental disasters. This study investigated the influence of FT cycles on the permeability of compacted clay through triaxial permeability tests, considering freezing temperature, cycle number, water content, and confining pressure. Scanning electron microscopy and nuclear magnetic resonance tests were performed to analyze the microstructure and pore characteristics of the clay during FT cycles. The results show that the hydraulic conductivity of the clay decreases significantly at high confining pressures due to soil consolidation. When the confining pressure exceeds 150 kPa, the impact of FT cycles on hydraulic conductivity becomes negligible. The increased number of FT cycles, exposure to lower freezing temperatures, and higher water content lead to more pronounced soil structure damage, resulting in a substantial increase in hydraulic conductivity. FT cycles cause macropores and microcracks to form and increase the average pore radius, creating preferential seepage pathways. Correlation analysis indicates that the increase in macropore content under various FT cycles is the primary reason for the increased hydraulic conductivity. Based on the modified Kozeny-Carman equation, a prediction model is developed to effectively estimate the hydraulic conductivity. These results provide valuable insight into the damage mechanism of clay permeability in seasonally frozen regions from a microscale perspective.