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PbTe and PbSe are among the most promising thermoelectric materials used in the mid-temperature (400–900 K) power generation range. In these materials the efficiency increase in thermoelectric performance is critically related to the lowering of lattice thermal conductivity (κL), without compromising the electronic power factor. By means of state-of-the-art equilibrium molecular dynamics (EMD), we investigate heat transport in several nanostructured PbTe/PbSe models as a function of material morphology. Layered composites show a reduction of the average κL of about 35 % with respect to the bulk. The insertion of PbSe nanoparticles into a PbTe matrix, or viceversa PbTe into PbSe reduces κL by up to 45 % while in more anisotropic nanocomposites the reduction exceeds PbSe/PbTe alloys. Layered composites show the lowest lattice thermal conductivity in the direction of layer stacking, for which an optimal thickness is identified. Along this line we provide a full account of the impact of alloying and (sub)nanostructuring on heat transport for this important class of materials. Particularly anisotropic nano-dot morphologies and layered (sub)nanocomposites emerge as a paradigm for outstanding thermoelectric materials.