Dimple structure is an effective heat transfer augmentation approach on coolant channel due to its advantage on pressure penalty. The implication of secondary protrusion, which indicates protrusion with smaller dimension than dimple, will intensify the Nusselt number Nu inside dimple cavity without obvious extra pressure penalty. The objective of this study is to numerically analyze the combination effect of dimples and secondary protrusion. Different protrusion–dimple configurations including protrusion print-diameter Dp, protrusion–dimple gap P, and staggered angle α are investigated. From the results, it is concluded that the implication of secondary protrusion will considerably increase the heat transfer rates inside dimple cavity. Cases 4 and 6 possess the highest Nusselt number enhancement ratio Nu/Nu0 reaching up to 2.1–2.2. The additional pressure penalty brought by the protrusion is within 15% resulting in total friction ratio f/f0 among the range of 1.9–2.1. Dimpled channels with secondary protrusions possess higher thermal performance factor TP, defined as (Nu/Nu0)/(f/f0)1/3, among which cases 4 and 6 are the optimal structures. Besides this, the TP of protrusion–dimple channels are comparable to the other typical heat transfer devices, and higher TP can be speculated after a more optimal dimple shape or combination with ribs and fins.