The hydraulic performance of geosynthetic clay liners (GCL) is closely related to the swelling characteristics of the bentonite particles and the resulting porous medium. However, there currently needs to be more analysis at the mesoscopic level to understand the permeating mechanisms. A numerical model using COMSOL was developed to study the effects of particle swelling on the effective porosity, tortuosity, and hydraulic conductivity of GCL under deionized water actions. The results demonstrate that the swelling of bentonite particles is a crucial factor influencing the effective porosity, tortuosity, and hydraulic conductivity of GCL. Particle swelling significantly affects the width and number of flow paths. When the hydraulic conductivity of GCL approaches the order of 10−11 m /s, a distinct main flow path exists. With an initial porosity increasing from 0.5 to 0.6, the effective porosity after particle swelling rises from 0.07 to 0.11. The width of the minor flow path is approximately 0.001 mm, which is about 2 500 times the size of a water molecule. As the bentonite particles swell, the tortuosity of the main flow paths within the GCL gradually increases. For an initial particle size of 0.1 mm and an initial porosity rising from 0.5 to 0.6, the tortuosity of the main flow path ranges from 1.2 to 1.4. However, the variation in tortuosity for all initial porosities is around 0.07. Meanwhile, when the hydraulic conductivity of GCLs approaches the order of 10−11 m /s, the bentonite particle swelling significantly affects the permeability of GCL. After the pore’s swelling ratio exceeds 0.96, a 0.01 increment in the pore’s swelling ratio results in a rapid decrease in the hydraulic conductivity of GCLs by one order of magnitude. These findings shed light on the mesoscopic behavior of GCL hydraulic performance, particularly the influence of bentonite particle swelling on the effective porosity, tortuosity, and hydraulic conductivity of GCL.