Dimple and protrusion play important roles in the heat transfer enhancement and flow characteristic in cooling channels, which widely employed within electronic cooling systems. Non-Newtonian fluid has significant differences with Newtonian fluid, such as water, in fluid characteristic. In this study, an experiment on the viscosity of three different kinds of non-Newtonian fluids, i.e., xanthan gum solution, Carbopol 934 solution, polyacrylamide solution, was first accomplished to acquire the viscosity with different mass fractions. Then, experimental measurements on heat transfer and friction characteristics of non-Newtonian fluid in a rectangular channel with dimples and protrusions were conducted. The overall Nusselt numbers (Nu) and Fanning friction factors at different dimple/protrusion structures were obtained with various inlet flow rates and mass fractions. The results show that only xanthan gum solution has the significant shear thinning effect within the concentration range of this study, and the dimples/protrusions both have great effect on the heat transfer enhancement in the rectangular channel, and that the heat transfer of the case with the protrusions and crossing arrangement can be further enhanced with the higher Nu when compared to the case with the dimples and aligned arrangement. Moreover, an increase in Nu with the higher non-Newtonian fluid mass fraction is observed.