In the present study, the detailed flow structure and heat transfer characteristics in the newly-designed heat transfer surface geometry were investigated. The surface geometry proposed in the present study is a traditional dimple structure combining with a protrusion inside the dimple, which is named a protrusion-in-dimple in this study. The basic idea underlying the present surface geometry is to enhance the flow mixing and the corresponding heat transfer in the flow re-circulating region generated by a conventional dimple cavity. The present study was performed by the direct numerical simulation at a Reynolds number of 2800 based on mean velocity and channel height and Prandtl number of 0.71. Three different protrusion heights for protrusion-in-dimples were considered as the main design parameter of the present study. The calculated pressure drop and heat transfer capacity were assessed in terms of the Fanning friction factor and Colburn j factor. The overall performances estimated in terms of the volume and area goodness factor for protrusion-in-dimple cases were higher than the conventional dimple case.