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The micro pin fin heat sink has great application potential in the heat dissipation of high-power LED chips, phased array radars and semiconductor lasers. The onset of nucleate boiling (ONB) is a critical limit in designing heat dissipation systems. A simultaneous visualization and measurement study is conducted to investigate the ONB phenomenon of deionized water in circular, diamond, and oval micro pin fin heat sinks. Experiments are conducted under inlet subcooling of 29.6–49.5 °C, mass flux of 147.4–355.4 kg m−2 s−1 and heat flux of 4.8–55.8 W cm−2. Visualization result indicates that the ONB is always initiated at the surrounding region of a micro pin fin. The effects of additional nucleation sites caused by a micro pin fin and the temperature distribution of the surrounding region captured by an infrared camera can be used to explain the occurrence of the first bubbles. In this study, the effects of inlet subcooling, mass flux, and the cross-section shape of the micro rib on the ONB characteristics are investigated. Results show that the heat flux and wall superheat needed for the ONB increase as the mass flux and inlet subcooling increase. Moreover, the heat flux required for the ONB in the diamond and oval micro pin fin heat sinks is higher than that in the circular one. On the basis of the experimental data, the correlation of heat flux at the ONB in the micro pin fin heat sink is established, with 85.7% of the data falling within an error band of ±15%.