The mesoscale mechanism of the interface behavior of different geomembranes was analyzed systematically combining with the mechanical model test of the Horizontal-Vertical (H-V) three-dimensional (3D) and traditional horizontal geomembrane by using the Particle Flow Code (PFC) based on the discrete element theory. The mesoscale characteristics such as the displacement variation， contact force distribution between the different kinds of geomembrane liners and soil particles, the stress distribution on the geomembrane, and the vertical stress distribution in the liner system were analyzed by comparing with the macroscopic mechanical characteristics obtained from the model test. The results show that the horizontal-vertical three-dimensional geomembrane provided similar friction as the traditional horizontal geomembrane. The vertical membrane of the H-V 3D geomembrane provided additional side friction and confine force. The vertical element not only confined the displacement and contact force of the partial transferring from the center to the two sides of the footing, but also provided the squeezed region between the H-V geomembrane and soil. This delayed the happening of the continuous slip surface and homogeneously distributed the stress in the H-V geomembrane lines. Therefore, the overall and uneven settlement of the H-V 3D geomembrane liner are smaller than the traditional under the same overburden load.