Tests using three prototype sub-scale engines in HYPR (Super/Hyper sonic Transport Propulsion System) project (HTCE (High Temperature Core Engine), HYPR90-T (Turbofan jet engine) and HYPR90-C (Combined cycle engine) ) were conducted to verify the technologies for the propulsion system of a hypersonic transport. Simulations using CFD (Computational Fluid Dynamics) were introduced to assess the component design to make sure that the intended performance would be achieved in the engine tests, and to support the interpretation of phenomena observed in the tests. In this paper, the following examples of the CFD applications are shown: three dimensional unsteady flow analyses of a single stage high pressure turbine including hot streaks from combustion cambers, axisymmetric steady flow analyses around disc cavities of a high pressure compressor, three dimensional flow analyses of a rim rear cavity with exit guide vanes and three dimensional steady flow analyses of turbine disc cavity of high pressure turbine.