In this study, flow structure in a two-stage centrifugal compressor for a turbo-chiller with the refrigerant, R134a, was numerically investigated at the design point of the compressor using a commercial code. Flow characteristics in the passages of impeller, diffuser and return channel were analyzed in detail including velocity vector, secondary flow, Mach number and pressure contours in blade spanwise and meridional plane for each stage. The estimation on the one-dimensional output from the preliminary design and three-dimensional shape of the impeller blade and the meridional shape of the return channel were performed through the flow analysis, while some numerical schemes and techniques including Multiple Frames of Reference technique, real gas property data and inlet boundary condition changes, which were used in CFD, were compared with their features. The results will be used as reference data for a new design of 3-D impeller shape to improve R134a compressor performance.