Pillar microchannel heat sinks have been widely used for chip cooling, while their overall heat transfer performance is restricted by the stagnation flow in pillar wake zone. In this work, a simple but effective method using slit microstructure modified on pillar was proposed to enhance wake zone heat transfer. It enables a special flow path for the incoming fluid that intensively disturbs the wake fluid. To validate the proposed method, a three-dimensional simulation was employed to study the laminar flow and heat transfer characteristics in the slit pillar microchannel. The pillar without slit design was also investigated for comparative analysis. Effects of slit angle (θ), height over diameter ratio (H/D), and blocking ratio (D/W) of a single pillar were systematically studied at the Reynolds numbers of 26–260. Results showed the case with θ = 0 deg always demonstrated lower surface temperature, higher Nusselt number and higher thermal performance index (TPI) compared to other cases with different slit angles at the same conditions. Furthermore, it was interesting to find that the slit configuration was not suitable for long pillar microchannel, but preferred for high blocking ratio pillar microchannel at present ranges (H/D ≤ 1, D/W ≤ 0.5). The slit pillar array microchannel was also explored and observed with improved overall heat transfer performance. The proposed slit microstructure well prevents the heat transfer deterioration in pillar wake zone, which is promisingly to be used for cooling performance improvement of electronic device.