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In this paper, direct numerical simulation (DNS) is carried out to investigate the flat plate boundary layer with heat transfer affected by a wake of a square bar. The bar is installed parallel to the plate and normal to the flow direction at the beginning of the boundary layer. The gap between the bar and the plate is varied in two cases. The fractional step method based on the Runge-Kutta and central difference schemes is used in the simulation. The instantaneous structures along with the statistical characteristics of the flow and thermal fields are presented and discussed. The results show that, in the large-gap case (C/d＝3.0), Karman vortices are shed from the bar and they perturb the boundary layer by advecting the fluid wallward and outward in turn. In the small-gap case (C/d＝0.25), however, the positive vortices shed from the lower side of the bar are small and the large negative vortices shed from the upper side of the bar dominate over the boundary layer, resulting in the strong backward sweep motions of fluid near the plate. Such motions contribute to the reduction in skin friction in comparison with the large-gap case. On the other hand, the thermal boundary layer in the small-gap case is strongly suppressed by the large negative vortices. This results in the larger temperature gradient and more active heat transfer in comparison with the large-gap case. These indicate that careful design is required to enhance heat transfer through a flat plate by utilizing a wake of a square bar.