Heat flux in electronic devices has increased dramatically with the development of advanced IC technology, facing the demand for effective thermal management technology. Micro pin-fin heat sink (MPFHS) has been demonstrated to be capable of improving the heat transfer capability and suppressing temperature rise effectively. In order to elaborate the discrepancy of heat dissipation of the MPFHS due to the cross-section shapes of pin-fin structures a set of heat sink samples with four different shapes, including the circle-MPFHS, the square-MPFHS, the crisscross- MPFHS, and the octagon-MPFHS, are fabricated with micromachining technology. Then, the thermal characteristics are tested by integrating the heat sinks with a Pt film resistor chip as the heating source, and nucleate boiling phenomenon was observed with a high-speed camera. Results showed that concave corners in pin-fin structures increased the specific surface area, but generated low velocity vortexes in back flow regions, reducing the heat transfer capability. The heat transfer coefficients of the octagon-MPFHS, the crisscross-MPFHS, and the circle- MPFHS was increased by 161.9 %, 152.4%, and 85.7 %, respectively, relative to the square-MPFHS at the flow rate of 147 kg/m2s. The heat transfer coefficients of the octagon-MPFHS, the crisscross-MPFHS, the circle-MPFHS, and the square- MPFHS was increased by 7.27%, 11.32%, 2.56%, and 4.76% when the mass-flow rate was increased from 147 kg/m2s to 295 kg/m2s. The nucleate boiling phenome-non in the crisscross-MPFHS showed periodicity and positive feedback effect, resulting in local dry-out and consequent heat transfer capability deterioration. This study will contribute to the design and modification of MPFHS.