The heat transfer in a pin finned duct is augmented by the protrusion in this study. The realizable k–ε turbulence model coupled with the enhanced wall function is used to obtain the flow structure and heat transfer characteristics. Six different rotational numbers (Ro = 0, 0.2, 0.4, 0.6, 0.8, and 1.0) and three different protrusion locations have been introduced. The pin fins and protrusions are placed on a simplified three-dimensional rectangular duct. Numerical results reveal that the Nusselt number in the pin finned channel has remarkable increase after adoption of the protrusions. In addition, the protrusion location and the rotational number have significant influence on the heat transfer distribution. The high rotational number is in favor of heat transfer enhancement on the endwall surface. Furthermore, the highest Nusselt number is occurred where protrusion is near the pin fin windward side.