This paper presents the effects of heat dissipation performance of pin fins with different heat sink structures. The heat dissipation performance of two types of pin fin arrays heat sink are compared through measuring their heat resistance and the average Nusselt number in different cooling water flow. The temperature of cpu chip is monitored to determine the temperature is in the normal range of working temperature. The cooling water flow is in the range of 0.02L/s to 0.15L/s. It’s found that the increase of pin fins in the corner region effectively reduce the temperature of heat sink and cpu chip. The new type of pin fin arrays increase convection heat transfer coefficient and reduce heat resistance of heat sink.