This study experimentally investigated the flow boiling of HFE-7100 in wavy copper microchannel heat sink (20 mm × 10 mm), which was fabricated with the ultrafast laser micromachining approach, consisting of 20 wavy microchannels with wavelength of 2000 μm and wave amplitude of 100 μm with triangular cross section (200 μm × 573 μm). The experiment was conducted with the mass fluxes of 330.07–550.11 kg/(m2·s) and heat flux of 14.5–411.3 kW/m2 at an inlet temperature of 15°C. Four flow patterns including bubbly flow, slug flow, churn flow and annular flow were captured with the visualization technique. Several confined bubbles with irregular shape were observed. In the low heat flux region, the dominant flow regime of heat transfer in the microchannels is the nucleate boiling and the heat transfer coefficient increases with increasing heat flux. With the nucleate boiling suppressed gradually, the evaporation of thin liquid film begins to dominate and the heat transfer coefficient decreases with the increase of heat flux. The heat flux has a significant effect on heat transfer coefficient compared with the mass flux and vapor quality.