In this work, we aim at exploring the effects of the germanium quantum dot (QD) layer embedded in silicon thin films on the thermal transport property in use of the non-equilibrium molecular dynamics simulation tool. An attempt is made to distinguish and understand the effect of the QDs themselves and the effect of the wetting layer on which QDs are grown. In this study, we notice as often observed a significant increase in the thermal resistance due to heterogeneous interfaces. Moreover, it is found that a simple QD interface has a thermal resistance monotonically decreasing with increasing quantum dot density. It is probably because the QDs make the transition from one material to another smoother, alleviate the acoustic mismatch, and thus assist the energy transport. When the germanium QDs together with a germanium wetting layer is inserted into a silicon material, the involved interface thermal resistance decreases first but increases later with increasing quantum dot density. The competition between the roughness effect and the wave interference effect is employed to explain this variation trend. As far as the quantum-dot superlattice thin film is concerned, we find its effective thermal conductivity decreases monotonically with increasing quantum dot density and with decreasing film thickness. In all cases, the size of quantum dots affects little on the thermal resistance/conductivity. (C) 2012 Elsevier Ltd. All rights reserved.