GCL composite vertical anti-seepage wall is a new type of vertical anti-seepage and the wall composed of cement bentonite slurry wall and geosynthetic clay liners (GCL). The overlap of the two GCLs has a potential impact on the decline of anti-seepage and pollution control performance of such anti-seepage walls, and there is currently a lack of analysis of such effects in research. A two-dimensional pollutant migration model was presented in this study, and the comprehensive analysis of the effect of GCL overlap width, B2, permeability coefficient of GCL overlap area, kp, the thickness Lw and permeability coefficient kw of cement-bentonite wall on the transversal distribution of pollutant and critical GCL overlap width were carried out on the basis of numerical simulation method. The calculation results showed that the GCL overlap width affected the distribution mode in the GCL composite vertical barrier wall, and increasing the B2 but not reaching the critical GCL overlap width (corresponding to the moment of pollutant breaking through the GCL overlap width and non-GCL overlap range) caused to the increase of breakthrough time of GCL composite vertical barrier wall. Generally, pollutant concentration at the inlet of GCL overlap area is higher than that at the outlet of GCL overlap area, especially for the scenario of the smaller kp or Lw, or the greater kp. The decrease of kp or kw resulted in remarkable reduction of the critical GCL overlap width, whereas the breakthrough time tends to be the same as that in the GCL composite cut-off wall with non-GCL overlap width. In addition, to increase the thickness Lw of cement-bentonite wall caused the decrease of the required critical GCL overlap width. Moreover, a two-fold increase in Lw from 0.4 m to 0.8 m caused a 2.5 times increase of the breakthrough time of GCL composite vertical barrier wall.