Flow boiling of dielectric fluids in microchannels is among the most promising embedded cooling solutions for high power electronics. However, it is normally limited by their poor thermal conductivity and small latent heat. To promote thin film evaporation and nucleate boiling, the side and bottom walls of five parallel microchannels were structured with nanowires in a silicon chip. A 10-mm-long thin-film heater was built-in to simulate heat source. Wall temperatures were measured from adiabatic condition to critical heat flux (CHF) conditions. Compared to the plain-wall microchannels with identical channel dimensions, heat transfer coefficient of HFE 7000 can be substantially enhanced up to 344% at the mass flux ranging from 1018 kg/m2s to 2206 kg/m2s as promoted evaporation and nucleate boiling. Moreover, pumping power was reduced up to 40% owing to the capillarity-enhanced phase separation. CHF was achieved from 92 to 120 W/cm2 and enhanced up to 14.9% at moderate mass flux of 1018 kg/m2s as a result of annular liquid supply. However, interestingly, this trend is non-monotonic and CHF is reduced at higher mass fluxes. This experimental study is trying to explore an optimal range of working conditions using nanostructures in flow boiling on highly-wetting dielectric fluids.