In view of the high vulnerability of the small islands of the Lesser Antilles to cyclonic hazards, realistic very fine scale numerical simulation of hurricane-induced winds is essential to prevent and manage risks. The present innovative modeling aims at combining the most realistically simulated strongest gusts driven by tornado-scale vortices within the eyewall and the most realistic complex terrain effects. The Weather Research and Forecasting (WRF) model with the nonlinear backscatter and anisotropy (NBA) large eddy simulation (LES) configuration was used to reconstruct the devastating landfall of category 5 Hurricane Irma (2017) on Saint Barthélemy and Saint Martin. The results pointed out that the 30 m scale seems necessary to simulate structures of multiple subtornadic-scale vortices leading to extreme peak gusts of 132 m s−1 over the sea. Based on the literature, such extreme gust values have already been observed and are expected for category 5 hurricanes like Irma. Risk areas associated with terrain gust speed-up factors greater than 1 have been identified for the two islands. The comparison between the simulated gusts and the remote sensing building damage highlighted the major role of structure strength linked with the socio-economic development of the territory. The present modeling method could be easily extended to other small mountainous islands to improve the understanding of observed past damage and to develop safer urban management and appropriate building standards.