Hydrothermal ore‐forming systems usually involve coupled processes among pore‐fluid flow, heat transfer, mass transport and chemical reactions in fluid‐saturated porous media. The finite element method (FEM) has provided a powerful tool to solve hydrothermal ore‐forming problems associated with pore‐fluid convective flow. Depending on different interests of research, a hydrothermal ore‐forming system may be simulated at two different length‐scale models, such as a regional (i.e., large length‐scale) model or a deposit (i.e., small length‐scale) model. However, there is an unsolved issue to guarantee the consistency between the applied boundary conditions to a deposit model and the predicted results, at exactly the same location as the boundary of the deposit model, from using the regional model. This paper proposes a FEM‐based dual length‐scale simulation procedure to address this issue. In the proposed procedure, a regional model of coarse mesh is first simulated by the FEM. Since a deposit model is located within the regional model, the applied boundary conditions to the deposit model of fine mesh can be determined from the simulation results of the regional model, so that the consistency can be guaranteed at the common boundary between the deposit model and the regional model. Main outcomes of this study have demonstrated that: (1) the proposed FEM‐based dual length‐scale simulation procedure is suitable and applicable for solving coupled problems involving pore‐fluid flow, heat transfer, mass transport and chemical reactions in fluid‐saturated porous media; (2) the proposed procedure is predictive because it is unnecessary to know the location of an ore deposit prior to the simulation of a hydrothermal ore‐forming system; (3) the boundary condition of a deposit model of fine mesh is consistent with the simulation results obtained from the regional model of coarse mesh, so that the reliability of the simulation results obtained from the deposit model can be ensured.