In the present study, we investigate heat transfer characteristics of a cross-cut heat sink and how the cross-cut changes the flow fields, which is strongly related to the heat transfer coefficient. The effects of the input heat flux, fin height, and difference of base thicknesses of upper and bottom heat sink on thermal performance are investigated. The tested heat sink system consists of 4 heat sinks. The heat sink base thickness of upper part is lower than that of bottom part. The flow characteristics in the heat sink system are investigated by numerical simulation tools and it is validated by experiments. The thermal performance of the cross-cut heat sink is approximately 10% better than that of the plate fin heat sink when the cross-cut is located at the point where the difference between the heat sink base thickness occurs. The effect of the cross-cut is significant when fin height is low. In conclusion, the cross-cut improves the thermal performance in the natural convection when the base thickness difference exists.