A continuous electron beam scanning process was used for the surface treatment on U-5.5Nb alloy, under various combinations of beam current, beam accelerating voltage, and scanning speed. The transverse cross-section characteristics of the resulting modification layers were metallographically measured to investigate the relationship between the electron beam processing parameters and the fusion zone geometry or the resolidification microstructure. Results showed that the resolidified modified layers were obtained with the bulk energy density (E0*) value exceeding 60.7 J/mm3. An “equiaxed-columnar-equiaxed” sandwich-type grain structure was formed in the resolidification fusion zone under the effects of local temperature gradient (G) and the growth rate (R). Different from that of traditional surface modified alloys, the cross-sectional microstructure of surface modified U-5.5Nb alloy consists of four characteristic areas: fusion zone (FZ), heat affected zone (HAZ), base metal (BM), and partially fusion zone (PFZ). The width (W) and depth (D) of the fusion zone had an almost linear increase with the bulk energy density (E0*). The Vickers hardness, Nb composition, and phase microstructures were also examined. The surface hardness values increased significantly following surface treatment, which was mainly attributed to phase transformation.