Defect-induced leakage of geomembranes may have negative effect on the anti-seepage safety of geomembrane faced earth-rock dams. Finite element theory of saturated-unsaturated seepage was employed for the 3D simulation of the seepage field of a typical geomembrane faced earth-rock dam in the condition that defects are in random distribution on the upstream dam surface. The quantity, types, location, sizes and distribution of geomembrane defects were considered reasonably, and the change rules of infiltration capacity, defect-induced leakage and phreatic line were analyzed emphatically. The results indicate that in the condition that the geomembrane is intact, the seepage flux changes little for both single and multiple defects on the geomembrane. However, when the geomembrane is under multiple defects, the defect-induced leakage increases significantly, leading to the increase of total seepage flux. Multiple defects will raise the phreatic surface in the dam body, and the variation of local phreatic surface height is related to the quantity and location of the defects. The more and lower the defects are, the more obvious the uplift of the phreatic surface can be. Further, the local distribution of water head behind the geomembrane is related to the cross effect of leakage of adjacent defects.