Thickened tailings deposition technology can form a stack with a certain slope by depositing high-concentration tailings slurries to reduce the footprint of tailings storage facilities and water consumption. Thickened tailings slurries exhibit complex non-Newtonian behaviors. Predicting the beach profile evolution of thickened tailings is important for the tailings storage facility design and management. A novel governing differential equation (GDE) derived from the lubrication theory is proposed in this work to capture laws of beach profile formation. Experimental data from three-dimensional laboratory-scale flume tests are analyzed using the proposed GDE. The GDE avoids the discrepancy from an inappropriate coordinate system, which exists in some state-of-the-art models and exhibits higher accuracy when predicting the beach shape near the toe of a preexisted layer. Compared with the Herschel–Bulkley (H–B) model, the Zhang’s equilibrium rheological model is preferred to determine the static yield stress, which leads to the accurate estimation of the stack profile in single- and multilayer thickened tailings depositions. The in-situ beach profile of thickened tailings is predicted using a numerical technique. A case study is included to demonstrate that the prediction based on the proposed GDE is consistent with the field measurement. The beach profile prediction of thickened tailings considering thixotropy is also discussed in this study. Results indicated that the decrease of yield stress along the flow path due to thixotropy leads to the concave beach shape of thickened tailings.