Nature inspired superhydrophobic surfaces are applied to microchannels to minimize the pumping power needed for driving the fluid flow. Special attention is given to the superhydrophobic surfaces with alternative microstructures and four different micro-structured configurations including square and triangular micro-posts and micro-holes are examined in aligned and staggered patterns. A numerical study is conducted to identify the impact of cavity fractions of 0.1–0.9 and Reynolds numbers of 10 and 100 on the performance indicators. These include drag reduction, heat transfer rate and mixed hydraulic and thermal behavior of the microchannel evaluated by the thermal performance index. The results reveal that the Poiseuille and Nusselt numbers decrease by the increase of cavity fraction. It is also observed that the triangular patterns feature the best thermal performance. The optimal combination of heat transfer and pressure drop, reflected by the goodness factor, can be achieved in staggered square holes and posts patterns at low and high Reynolds numbers, respectively. Considering the total thermal performance of the microchannel, changing the microstructures from aligned to the staggered pattern can have a significant influence upon the square micro-posts and micro-holes but only a modest impact on the triangular posts. Nonetheless, the optimal surface configuration should be picked up in accordance with the specific application in hand and by prioritizing improvements in the thermal or hydraulic performance of the microchannel.