The slit pillar allows a small fraction of the mainstream flow through pillar to disturb the pillar wake zone fluid and eventually enhance the local and global heat transfer performances in microchannels. In this study, three-dimensional full-domain numerical simulations on the hydrodynamic and thermal characteristics of slit pillar array in microchannels are performed. Effects of slit angle and height over diameter (H/D) ratio on the fluid flow and heat transfer are studied. Comparisons with the nonslit pillar array are conducted on pressure drop, surface temperature, Nusselt number, and thermal performance index (TPI). Furthermore, the results are analyzed by using the entropy generation. As a result of secondary flows and enhanced convective heat transfer area, all cases at H/D ratio of 0.3 demonstrate enhanced heat transfer performance at an increase of 18.0–34.7% on Nusselt number, while a reduction of 3.4–12.9% on pressure drop in comparison to the criterion case at the same conditions. Among them, slit 15–15 deg shows the best comprehensive heat transfer performance. Due to the improved uniformities of velocity and temperature distributions, all slit pillar array microchannels show decreased entropy generation. The maximum entropy generation reduction can reach up to 15.8%, as compared with the criterion case at the same conditions. The above results fully demonstrate that the novel slit pillar array microchannel heat sink can be used as an effective approach for heat transfer enhancement.