Nanoimprint lithography has attracted broad interest as a low cost method to define nanometer scale patterns in recent years. In the cooling stage of the nanoimprint lithography process, the polymer resist is constrained inside the tool. As the temperature decreases, the polymer may shrink away from the tool. However due to the constraint of the tool, thermal stresses may be induced in the polymer while the relaxation effect tends to release the build up of the stress level at the same time. In this study, a visco-elastic model was developed to analyze the stress variations of the imprinted patterns during the cooling process. Most of the residual stress is found to concentrate on the interface between the polymer resist and the substrate. Also, some stress concentration areas are observed near the adjacent of the large un-patterned area and the pillar Thermal stress above the glass transition point is demonstrated to be able to relax during the cooling process. Most of the residual stresses are induced at the cooling stage with a temperature lower than the glass transition point.