In this study, heat transfer characteristics and dynamic flow boiling instabilities of ethanol were investigated experimentally in a rectangular microchannel with 1000 μm wide, 200 μm deep, and 30 mm long. The local temperature, pressure, and mass flux were recorded at a sampling frequency of 1 kHz in synchronism with high-speed visualization of up to 2000 frames/s enabling transient characterization of the flow boiling behavior. Mass flux and heat flux ranged from 30 to 50 kg m−2 s−1 and 10 to 120 kW m−2, respectively, with the inlet subcooling ∆Tsub = 25 °C. It is concluded that the inhibition of bubble nucleation which is caused by enlarged bubble in the confined space result in the deterioration of heat transfer performance. Flow boiling at higher mass flux present superior heat transfer because of much more effective bubble nucleation. The triggering of micro-channel flow boiling instability show strong dependency on quasi-periodical flow phenomenon with multiphase alternation other than the confinement bubble growth theory. Different frequency and amplitude types of fluctuations co-exist at lower mass flux. The thermo-physical properties of the working liquid significantly affect the fluctuation amplitude.