A discrete element method (DEM) is developed to simulate the heat transfer in granular assemblies in vacuum with consideration of the thermal resistance of rough contact surfaces. Average heat flux is formulated by the positions and heat flow rates of particles on the boundaries of the granular assemblies. Average temperature gradient is given as a best-fit formulation, which is computed from the relative position and temperature of particles. With the thermal boundary condition imposed on the border region, the effective thermal conductivity (ETC) of granular assemblies can be calculated from the average heat flux and temperature gradient obtained from DEM simulations. Moreover, the effects of particle size, solid volume fraction and coordination number on the ETC are also investigated. Simulation results show that granular assemblies with coarse particles and under large external compression forces exhibit a better heat conduction behavior. The effects of particle size and external compression forces on the ETC are in good agreement with experiment observations. (C) 2010 Published by Elsevier B.V.