The vortex structure of a separated flow over a backward-facing step controlled by a synthetic jet is investigated by using an implicit large-eddy simulation with a high-order compact difference scheme. The computation results show that mixing in the shear layer is not enhanced, when the flow is controlled at the normalized frequency of 2.0 based on the height of backward-facing step. In this case the separation length is similar to that in the case without flow control because weak and short periodic vortices are induced by the synthetic jet, and they weakly interact with the shear layer and diffuse in the recirculation region. On the other hand, the separation length becomes 20% shorter when the flow is controlled at F⁺_h = 0.2 than that in the case without flow control. Strong two-dimensional vortices generated from the synthetic jet interact with the shear layer, which increases the periodic component of the Reynolds stress within that layer. These vortices are deformed into three-dimensional structures, which strengthen the nonperiodic component of the Reynolds stress in the recirculation region.