Abstract: Leakage significantly impacts the operational and maintenance safety of reservoirs. The existing researches on the leakage due to defective geomembranes remain at experimental stage, with limited exploration of numerical simulation methods specifically focused on impermeable reservoirs with defective geomembranes. Many challenges associated with geomembrane defective seepage were elaborated upon. Based on the characteristics of seepage through defective geomembranes, an inverse simulation method was proposed, which uses the defective geomembrane and its contact layer as the seepage control layer, termed the impermeable layer with defective geomembranes. Based on the monitoring data of leakage in the Xixia Reservoir over a period of 1360 days, a three-dimensional seepage model of the impermeable reservoir with defective geomembranes was developed. The equivalent permeability coefficients of impermeable layer with defective geomembranes were back-calcualted and validated using data from ten operational periods of the Xixia Reservoir. The validation showed that the research method was reasonable and revealed that with the operation of the reservoir to the dynamic high reservoir level, the equivalent permeability coefficient of the impermeable layer with the defective geomembrane consists of three phases of decreasing, increasing and stabilizing, which was in line with the law of infiltration and deformation of coarse-grained soil under the geomembrane and corresponded to the three phases of the seepage pressure and the seepage pressure drop in the monitoring points under the geomembrane. Research resulted provide technical support for the evaluation of safe operation of geomembrane impermeable reservoirs.