Nanoimprint lithography (NIL) has attracted broad interest as a low cost method to define nanometer scale patterns in recent years. A major disadvantage of thermal NIL is the thermal cycle, that is, heating over glass transition temperature and then cooling below it, which requires a significant amount of processing time and limits the throughput. One of the methods to overcome this disadvantage is to improve the cooling performance in NIL process. In this paper, the performance of the cooling system of thermal NIL is numerically investigated by SolidWorks Flow Simulation program. The calculated temperatures of nanoimprint device were verified by the measurements. By using the analysis model, the effects of the change of flow velocity and cooler location on the cooling performance are investigated. For the 6 cases (0.1 m/s, 0.5 m/s, 1 m/s, 3 m/s, 5 m/s, 10 m/s) of flow velocity and for the 6 cases of distances (50 mm, 40 mm, 30 mm, 20 mm, 10 mm, 1 mm) of cooler location, the heat conjugated flow analyses are performed and discussed.