Combined with the mechanical model test of interaction between soil and liner of H-V （Horizontal-Vertical）three-dimensional geomembrane and traditional horizontal geomembrane, particle flow code based on discrete element theory was used to analyze the micromechanism between the soil and the geomembrane with different geometric characteristics. Thus, the micromechanism of improving the macro mechanical effect of H-V three-dimensional geomembrane liner is proved. By comparing the macroscopic mechanical characteristics obtained from the model test of geomembrane composite liner, the article mainly studies the displacement change law between soil particles and geomembrane liner with different geometric characteristics, the contact force distribution between soil particles and geomembrane, the stress distribution on the geomembrane, and the vertical stress distribution in the integral liner system from the micro perspective. It is found that, compared with the traditional horizontal geomembrane, the H-V three-dimensional geomembrane has not only the friction between the traditional horizontal geomembrane and the soil but also the side friction and bite force of the vertical membrane on the soil particles. The vertical membrane can restrain the displacement of soil particles and the transmission of force chain from the load center to both sides, and make the H-V three-dimensional geomembrane and soil form a good constrained compaction area. This can not only delay the formation of continuous slip surface in the H-V three-dimensional geomembrane liner, but also more effectively homogenize the stress distribution in the integral liner, so that the H-V three-dimensional geomembrane liner has smaller overall settlement and uneven settlement under the same overlying load.