In this paper, the influence of film thickness on the layer instability mode of a thin polymer bilayer (poly(methylmethacrylate) (PMMA)/polystyrene (PS)/Si substrate) has been investigated. The experimental results show that kinetic forces can greatly influence the instability process of the thin polymer bilayer. In the case of PS-2.4K (M w-PS ¼ 2.4 kg mol ), only the PMMA layer ruptures on the PS layer and the dewetting process is a thermodynamically controlled one. Besides, the influence of the instability mode on the template-assisted dewetting process of the thin polymer bilayer also was studied. After annealing the pre-patterned bilayer, in the case of the kinetically controlled dewetting, the PMMA film bends to conform to the buried PS-PMMA interface and concave half cylinder grooves form during the dewetting process; however, in the case of the thermodynamically controlled dewetting, PMMA chains move to the top of cylinder stripes and obvious trenches are found after PMMA chains are etched. This proposes a simple method to obtain different surface structures by changing the instability mode of the thin polymer bilayer.