Stepped dumpling of waste is the main operating method used in landfill engineering. For the liners located at the bottom of the landfill, the waste can be considered as a vertical loading due to its heavy weight, causing compressive deformation of the liners and, most importantly, tending to lose the effectiveness of the geomembrane with the differential deformation. However, most experiments or numerical models use transient‐loading and ignore the influence of variable step‐loading on liner performance. In this study, a one‐dimensional fully coupled hydro‐mechanical‐chemical (HMC) model for contaminant transport under the framework of small strain, taking into account the step‐loading effect, is proposed, and its analytical solutions are derived by using the separation of variables. The behavior of contaminant transport in a single‐layer clay liner is investigated under variable step‐loading conditions. Analytical results show that the step‐loading can significantly accelerate the transport of contaminants compared to the transient‐loading. Variation of the step‐loading rate from 2 to 4 times yields an increase of 6.1 and 15.2 years of the breakthrough time. At a step‐loading rate of 50 kPa/year, the breakthrough increases by 13.37 years, and the peak settlement reduces to half that under transient‐loading. Ignoring the influence of step‐loading on contaminant transport may overestimate the performance of clay liners.