As an essential foundation for the associated thermoelasticity analysis in the boundary element method (BEM), this article proposes an expedient, yet powerful, approach to analyze the heat conduction in multiply jointed anisotropic media with bonding defects/interface cracks. The direct domain mapping technique (DDM) is applied to treat a domain consisting of dissimilar anisotropic sub-regions in the potential theory of BEM. The heat transfer across a crack is modeled with a gap conductance equation specially formulated for the BEM analysis. Two numerical examples are provided as illustrations of the validity and the applicability of this proposed scheme.