In this paper, a combined transport-defect evolution multiscale model describing the generation and the evolution of microstructure damage in silicon carbide (SiC) induced by focused helium ion beams is developed. In the proposed model, the transport of helium ions and displaced atoms in the SiC substrate and the generation of point defects are described by the Boltzmann transport equations, while the subsequent defect evolution is characterized by a set of rate equations with the contributions of the modeling of the bubble coalescence as well as the substrate swelling. The validity and superiority of the transport equations are verified by comparing the simulation results with the data from experimental measurements and available simulation methods. The subsurface amorphous profile, onsurface swelling profile, and the spatial and size distribution of helium bubbles in a SiC substrate irradiated by focused helium ion beams are simulated using the proposed multiscale model. The damage morphology simulated by the proposed model is in good agreement with the transmission electron microscopy images at different beam energies and doses. This work provides an effective tool for full-stage modeling of complex evolutionary mechanisms of microstructure damage induced by precise and high-throughput helium irradiation.