This paper shows which morphological characterization method is most appropriate to simulating membrane performance in sweeping gas membrane distillation in the case of multilayer hydrophobized ceramic membranes. As a case study, capillary four-layer hydrophobic carbon-based titania membranes arranged in bundles in a shell-and-tube configuration were tested with NaCl-water solutions using air as sweeping gas, operating at temperatures from 40 to 110 °C and at pressures up to 5.3 bar. Contrary to what is generally performed for polymeric membranes and also suggested by other authors for ceramic membranes, the mass transfer across the membrane should be simulated using the corresponding values of the mean pore diameter and the porosity-tortuosity ratio of each layer and measured by the layer-by-layer (LBL) method. Comparison of the modeling results with experimental data highlights that the use of parameters averaged over the entire membrane leads to an overestimation by a factor of two to eight of the modeled fluxes, with respect to the experimental values. In contrast, the agreement between the modeled fluxes and the experimental values is very interesting when the LBL parameters are used, with a discrepancy on the order of +/−30%. Finally, the model has been used to investigate the role of operative parameters on process performances. Process efficiency should be the optimal balance between the concomitant effects of temperature and velocity of the liquid phase and pressure and velocity of the gas phase.