This study is focused on the mechanism of propagation of tip clearance flow and corner separation of a high speed, low Reynolds number millimeter size centrifugal compressor passage in a situation with high temperature wall. The physical basis of increasing tip clearance vortex and corner separation vortex, on blade suction surface, is explained by the severe effects when heat transfer is considered through high temperature wall. Furthermore it induces severe performance deterioration in micro compressor. In this paper, an isothermal blade temperature boundary condition is applied for a comparison with adiabatic case. A series of steady three dimensional RANS numerical simulations are carried out to study the secondary flow characteristics through detailed analysis of typical flow features. CFD results show a decrease in compression capability and drop in efficiency due to a large tip clearance vortex and a large corner separation vortex, caused by an absolute velocity change when flow passes through heated passage. Therefore a favorable Mach number distribution is also discussed to achieve a high performance of high temperature silicon based micro compressor.