Cooling technology is very important for the safe operation of nuclear power plant. Microchannel heat exchangers have been treated as one of the most potential cooling technologies. Flow characteristics of microchannels (hydraulic diameter is 100 μm) with a new structure, with which obstructions were placed along channels walls, have been investigated under the consideration of the effect of compressibility and viscosity heating. The influences of the Reynolds number, obstruction height, pitch, and geometry and width height ratio on the flow characteristics are investigated. It indicated that Poiseuille number increased with the increasing of Reynolds number and second order increasing with obstruction height. It was observed that the obstruction pitch is an important design parameter for flow characteristics, the pressure drop decreased with the increase of the obstruction pitch. The Poiseuille number reaches maximum for triangular obstruction and minimum for semicircle obstruction. It is also found that width height Ratio of obstruction plays an important role, Poiseuille number will obviously increase when width height Ratio of obstruction is bigger than 1.