The thermal hydraulic performance of a double-layer microchannel heat sink was analyzed with a variety of channel shapes using three-dimensional Navier-Stokes equations in a range of Reynolds numbers from 160 to 850. Parallel and counterflow arrangements of double-layer microchannels and seven cross-sectional shapes of microchannels (boot, diamond, hexagonal, pentagonal, rectangular, rectangular wedge, and triangular) were tested in this work. The temperature, Nusselt number, thermal resistance, and pumping power were obtained for each channel shape and arrangement using conjugate heat transfer analysis. Among the tested microchannel shapes, the rectangular wedge shape showed the best thermal performance with the lowest thermal resistance and also with the greatest pumping power. The counterflow arrangement showed better thermal performance with a similar pumping power than the parallel flow arrangement for all the channel shapes.