Abstract: In this paper,the flow and thermal transport equations for the accurate description of natural thermal advection in the process of heat transfer in aquifers are manipulated and presented.A nonlinear three-dimensional heat transfer model is established as well.According to the characteristics of the model,the DouglasBrian ADI finite difference scheme,the characteristic reverse-tracking technique,and the improved Picard iterative method are proposed to solve it,and the calculation steps are also provided.Finally,the model together with the numerical methods are applied to simulate a multi-well RTES(Aquifer Thermal Energy Storage) experiment which was performed in the second confined aquifer in Shanghai.The results are satisfying and the natural thermal advection in the experiment is well represented.This shows that the model is reasonable and reliable,and the proposed methods are quite effective.