In order to observe the thermal-dissipation capability of water-cooling heat sink, the thermal resistance of water-cooling heat sink is calculated and deduced theoretically under different flow rates. The water-cooling heat sink inside was constituted of many rectangular series and parallel channels. To improve the calculation efficiency, water-cooling heat sink model was simplified symmetrically. The temperature distribution of heat sink was obtained by Computational Fluid Dynamics (CFD) simulation. The simulation results were consistent with that of the theoretical calculations very well. Finally, the tests of water-cooling heat sink show that this method of calculation is reasonable, which can have an important significance for reference in the engineering design.