In this paper experiments have been conducted to investigate the flow boiling and heat transfer characteristics in microchannels with three different surface wettability. Three types of microchannels with a super-hydrophilic surface (θ ≈ 0°), a hydrophilic surface (θ = 43°) and an untreated surface (θ = 70°) were prepared. The results show that the average heat transfer coefficient of a super-hydrophilic surface microchannel is significantly higher than that of an untreated surface microchannel, especially when the mass flux is high. The visualization of the flow patterns states that the number of bubble nucleation generated in the super-hydrophilic microchannel at the beginning of the flow boiling is significantly more than that in the untreated microchannel. Through detailed analysis of the experimental data, flow patterns and microchannel surface SEM images, it can be inferred that the super-hydrophilic surface microchannel has more active nucleation cavities, a high nucleation rate and a large nucleation number, a small bubble departure diameter and a fast departure frequency, thereby promoting the flow and heat transfer in the microchannel. In addition, through the force analysis of the vapor-liquid interface, the mechanism that the super-hydrophilic microchannel without dryout under high heat flux conditions is clarified.