The pile-soil-raft interaction and thermo-mechanical effects lead to broad attention in the analysis of the energy piled raft foundations. Natural soils are generally anisotropic and show obvious stratification. Influences of the cross-anisotropy and stratification on the performance of energy piled raft foundations are investigated in this paper. The raft and energy piles are modelled as a flexible plate and one-dimensional bars, respectively. Stiffness matrix equations of the raft and energy piles considering the thermal and mechanical loads are established based on the finite element method. The soils are modelled as the layered cross-anisotropic elastic media. The force-deformation relationships of nodes at the raft-soil and pile-soil interfaces are acquired based on the boundary element method. Then, displacement variables of the pile-soil interface onto the raft are condensed and the pile-soil-raft interaction is further simplified into the raft-soil interaction. The comparison with in-situ tests is made to verify the proposed method. Parametric analyses show that the top axial force of the center pile increases by approximately 5 % in the cooling condition and 12 % in the heating condition with the increase of the cross-anisotropic parameter m*, while it makes a negligible contribution to that of the corner and side pile.