Three-dimensional turbulent channel flow and heat transfer in the presence of a square cylinder were investigated numerically for a Reynolds number of 3000. Turbulent flow was simulated using large eddy simulation in which the eddy viscosity was evaluated by a subgrid-scale model of structure function and selective structure function. The attached wall boundary layer of the channel starts to separate if an insulated cylinder is placed in the channel, and a subsequent recirculation zone appears downstream of the cylinder. Nusselt number distribution along the floor of the channel showed an increase in the downstream part of the cylinder with a relative maximum slightly downstream of the reattachment point. The position of the cylinder in cross-stream direction affects the heat transfer from the channel wall. This quantity increases with decreasing the distance between the cylinder and the channel wall. A correlation was developed for the mean total Nusselt number over the floor of the channel with the position of the cylinder in the channel.