Material properties, crucial design parameters in landfill cover systems, can exhibit spatial variability due to non-uniform particle size and uneven compaction, affecting cover performance. Additionally, cover thickness, another key design parameter, can induce stress variation and influence soil-water retention capability. Previous designs always ignored these uncertainties and stress effects, potentially leading to unreasonable design schemes. This study aims to provide design recommendations for a three-layer landfill cover system under heavy rainfall, considering these factors simultaneously by the random finite element method (RFEM). The stress effects are captured using a stress-dependent soil-water retention curve (SDSWRC) and the hysteresis in the SDSWRC is considered in probabilistic analyses. For practical applications, uncertainties in two easily controllable particle size parameters, D10 and D60, are depicted by copula-based cross-correlated random fields. Based on empirical equations, the spatial variability of SDSWRC and water permeability function (WPF) can be further characterised by D10 and D60 random fields. It is found that considering SDSWRC and its spatial variability (e.g., shape) can overestimate percolation by at least 1.7 times compared to deterministic analysis using SWRC. The spatial variability of SDSWRC shape has a more significant impact than spatially variable saturated water permeability on cover system performance. Among candidate copulas, the CClayton copula (survival copula of Clayton copula) yields the most conservative results due to its upper tail dependence. The particle size and thickness of the bottom layer influence the cover system performance more than the upper two layers. A bottom layer with D10≤ 0.009 mm and D60/D10≥ 7.54, and thickness ≥ 0.8 m is recommended to achieve a satisfactory performance level with a 100-year design life.