In this study, an analytical solution is proposed to describe one-dimensional self-weight consolidation of two-layer soil under variable load and semi-permeable boundary condition. The analytical solution is comprehensively validated against existing field test, analytical solution and numerical simulation results. The influence of drainage capacity of boundary, self-weight, load rate, and soil layering features are then investigated. The difference of consolidation ratio between the complete pervious boundary condition and the semi-permeable boundary condition decreases with increasing semi-permeability coefficient R. Considering the self-weight will increase the excess pore pressure and make the maximum pressure appear below the middle depth, especially at the early time. The effect will be weaker and weaker and finally disappear. The dissipation of excess pore pressure is significantly impeded if the soil layer with lower consolidation coefficient is at the bottom. Finally, the design curve of the time for practical completion of consolidation (t) is provided. An almost flat part can be observed in the curve if the relative thickness of the layer with lower consolidation coefficient ranges from 0.1 to 0.23, indicating that the influence of relative thickness on t is negligible over this range, which provides a helpful reference for two-layer soil consolidation in engineering practices.