The feed mass and the filter‐press mass per cabinet (FMP) are uncertain variables in the thickening‐dewatering (TD) process. These uncertain variables must be considered for the optimization; otherwise, the energy economic index (EEI) and the safety risks will increase. Therefore, in this paper, a two‐layer chance‐constrained optimization model for the TD process with uncertain variables is proposed. The optimization model is a sample average approximate‐expected value model (SAA‐EVM), and scenarios are generated by Monte‐Carlo simulation. To reduce the computational time, the optimization model is divided into a two‐layer chance‐constrained optimization model. The computational time is reduced by reducing the dimensions of the decision variables. Simulation results show that this two‐layer chance‐constrained optimization model can reduce the EEI and safety risks and improve the stability of the process, while the computational time meets the requirements of mineral processing plants.