Abstract: Freestream fluctuation has a direct impact on the experiments carried out in hypersonic wind tunnels, due to effects such as hypersonic laminar/turbulent boundary-layer instability and transition. In order to obtain a deep insight into the mechanism in the hypersonic boundary layer instability, it is significant to measure and quantify the freestream disturbance in the hypersonic wind tunnel. Upon this work, we propose a novel approach for the disturbance modes characterization such that the hypersonic freestream can be measured by the hot-wire anemometer and the Pitot probe simultaneously. All the amplitudes of the disturbance modes, such as the entropy, vorticity and sound wave modes, are derived based on the small disturbance assumption by using the transfer function for the Pitot probe, which is obtained from direct numerical simulation. This novel approach for disturbance decomposition in hypersonic freestream has been applied in the Mach 6 Ludwieg tube wind tunnel at Technical University of Braunschweig in Germany. The experimental results show that this Ludwieg tube tunnel is a typical noise wind tunnel, in which the acoustic mode is up to 69% of the total disturbance mode, and the vortex mode and entropy mode account for about 15% respectively. This disturbance mode decomposition method sheds light on the freestream disturbance measurement in the hypersonic wind tunnel and provides valuable data for hypersonic wind tunnel experiments.