The two-phase flow boiling in microchannels is an attractive cooling strategy for high-power density electronic/optoelectronic devices, while the exist of sub-millimeter “hot spots” characterized by ultra-high heat fluxes would degrade the reliability and safety for commercial and consumer applications. In this paper, the bubble nucleation and evolution characteristics of subcooled flow boiling in high aspect ratio flat microchannels were experimentally studied with the aid of high-speed visualization and infrared temperature measurement at localized heat fluxes exceeding 1.5 kW/cm2. Dielectric liquid HFE-7100 was used at mass flow rates ranging from 11.1 to 178.2 kg/(m2·s). Results show that the explosive boiling process was accompanied by an approximately linear bubble growth rate of about 20 m/s at about the first half of growth stage, and the time duration for overall bubble growth was less than 200 μs. The bubble nucleation was suppressed dramatically on the smooth bottom surface of the channel even at a localized “hot spot” heat flux above 2.5 kW/cm2. The introduction of staggered short micro-pin fin arrays at the bottom wall significantly lowered the threshold heat flux and onset temperature of bubble nucleation and reinforced the bubble growth to larger sizes. It is attributed to the reduction in the temperature gradient of thermal boundary layer adjacent to the heated wall, and it would be further reduced by increasing the micro-pin fin denseness. Even at quite high superheats on smooth and micro-structured surfaces, the heterogeneous boiling mechanism was proved to still work.