A series of COMSOL numerical models were developed to explore how confining pressure impacts the microscopic structure and hydraulic conductivity of Geosynthetic Clay Liners (GCLs), taking into account the bentonite swelling ratio, mobile porosity, pore size, and tortuosity of the main flow path. The study reveals that the mobile porosity and pore size are critical factors affecting GCL hydraulic conductivity. As confining pressure increases, the transition of mobile water to immobile water occurs, resulting in a reduction in mobile water volume, the narrowing of pore channels, decreased flow velocity, and diminished hydraulic conductivity within the GCL. Mobile porosity undergoes a slight decrease from 0.273 to 0.104, while the ratio of mobile porosity to total porosity in the swelling process decreases significantly from 0.672 to 0.256 across the confining pressure range from 50 kPa to 500 kPa, which indicates a transition of mobile water toward immobile water. The tortuosity of the main flow path shows a slight increase, fluctuating within the range of 1.30 to 1.36, and maintains a value of around 1.34 as the confining pressure rises from 50 kPa to 500 kPa. At 50 kPa confining pressure, the minimum pore width measures 5.2 × 10−5 mm, with a corresponding hydraulic conductivity of 6.2 × 10−11 m/s. With an increase in confining pressure to 300 kPa, this compression leads to a narrower minimum pore width of 1.81 × 10−5 mm and a decrease in hydraulic conductivity to 5.11 × 10−12 m/s. The six-fold increase in confining pressure reduces hydraulic conductivity by one order of magnitude. A theoretical equation was derived to compute the hydraulic conductivity of GCLs under diverse confining pressure conditions, indicating a linear correlation between the logarithm of hydraulic conductivity and confining pressure, and exhibiting favorable agreement with experimental findings.