The Flexible Combined Imager (FCI) is an instrument to be borne by the future geostationary meteorological satellite Meteosat Third Generation (MTG). A numerical simulator was set up to provide simulated outputs of the instrument. It includes top-of-atmosphere scene of upwelling spectral radiance obtained by a radiative transfer model in the clear atmosphere, and the transfer function of the FCI. The sensitivity of the sensor outputs to aerosol properties is studied by varying the inputs defining the scenes and their illumination. The Global Sensitivity Analysis (GSA) with the Sobol' decomposition is applied to the outputs of the simulator, yielding a ranking of the inputs with respect to their influence on the FCI numerical outputs. The results are presented for all visible and near infrared channels of the FCI for desert type of aerosols according to the OPAC database. The study highlights the most relevant channels for aerosol detection and characterization and gives assessment of the different sources of uncertainties in aerosol retrieval with such channels.