The High-Speed Flight Demonstration (HSFD) project is the latest in a series of flight experiments in a research program into reusable space transportation systems being conducted by JAXA. HSFD Phase II was a drop test from a stratospheric balloon to clarify the transonic aerodynamic characteristics of the HOPE-X configuration and to obtain data to validate wind tunnel tests and computational fluid dynamics (CFD) predictions. Since a phased flight experiment can not applied because of its launch method, it was necessary to establish a mathematical model as precise as possible and to conduct accurate flight simulation analysis beforehand. This paper describes the mathematical model of the experiment and the comparison between the results of flight simulation and the flight experiment.