This paper concerns the effect of leading edge boundary layer thickness on dimple flow structure and separation control. A flat plate with adverse pressure gradient sufficient for separation was designed. Large eddy simulation (LES) with dynamic Smagorinsky subgrid model was validated. Dimples with R=0.378, 0.994, 1.453 (R is the ratio of leading edge boundary layer thickness to dimple depth) were investigated. The results show that the horseshoe vortex dominates the dimple flow structure. As R increases, the head of the horseshoe vortex rises further away from the wall and moves downstream. Hairpin vortices in the dimple wake are productions of the horseshoe vortex. Both the horseshoe vortex and the hairpin vortices energize the boundary layer by mixing with the free-stream fluid. As R increases, the separation control effectiveness decreases.