Cooling technique in a miniscale heat sink is essential with the development of high-power electronics, such as electronic chip. As heat transfer techniques, jet impingement cooling and convective cooling by roughened surface are commonly adopted. To obtain a good cooling efficiency, the cooling structure within the heat sink should be carefully designed. In the present study, the miniscale heat sink with a feature size of 1–100 mm is setup. Arrangement of the jet impingement and dimple/protrusion surface is designed as heat transfer augmentation approaches. The effect of dimple/protrusion configuration and depth to diameter ratio is discussed. From the result, the heat transfer coefficient h distribution of heat sink surface is demonstrated for each case. The pressure penalty due to the arrangement of roughened structure is evaluated. Also, thermal performance (TP) and performance evaluation plot are adopted as evaluations of cooling performance for each configuration. Comparing all the cases, optimal cooling structure considering the energy-saving performance is obtained for the miniscale heat sink. Referencing the statistics, a new insight has been provided for the design of cooling structure inside the miniscale heat sink.