In the flight flutter test of a certain type of aircraft, frequency sweep excitation generated by control surfaces was adopted. Due to the limitation of the flight control, the sampling rates of the sweep excitation and the response measurements are inconsistent, which leads to difficulties in performing the experimental modal analysis. To solve this problem, the Frequency-Spatial Domain Decomposition (FSDD) method has been investigated in this research, since FSDD method is able to identify modal parameters from response measurements only, without using the excitation signals. This research validates the applicability of the FSDD method to systems under sweep excitation, using simulated signals from a typical cantilevered beam model. The method has also been tested on the flight flutter test data and has been proved to be feasible and effective in flutter modal analysis.