In a large area magnetron sputtering system, which is under the influence of high heat load from the plasma, it is necessary to use the effective water cooling in order to maintain the proper deposition performance and the economic use of target materials. A series of three-dimensional numerical simulations are carried out on the simplified model of the large area magnetron sputtering system with the cooling plate that includes the U-shaped water channel. The analysis is focused on the effects of water channel geometry, cooling water flowrate, thermal conductivity of target material, and the degree of target erosion on the cooling performance of cooling plate, which is represented by the temperature distribution of target material.