It is generally difficult to obtain good weld formation and excellent properties in super thick titanium alloy joints via conventional electron beam welding (EBW) methods due to the fact that the melt pool flow becomes more unstable as the plate thickness increases. In this study, electron beam scanning welding (EBSW) was utilized to weld 100 mm Ti–6Al–3Nb–3Zr–1Mo titanium alloy plates to improve the weld formation and impact toughness through the scanning effect. The results revealed that there were spatter and cutting defects on the surface and inner pore defect in the normal EBW joint, which could be effectively eliminated via EBSW. The decrease of the amplitude of the fluid flow rate and the change of the velocity direction were mainly responsible for this. A large amount of lamellar α phase with similar orientation was formed in the fusion zone (FZ) due to the fast cooling rate. The joint coefficient for both EBSW and EBW reached 100%, with the joint tensile strength of ∼840 MPa. The impact energy of the FZ in the EBSW joint was 70.5 J, reaching 210.4% of that of the BM (33.5 J). The impact toughness increase ratio in this study was far larger than those for Ti alloy welds ever reported, which was mainly attributed to that the high angle α colony boundaries with high preferred orientation in the FZ deflected the crack propagation direction. This study provides a reference for the strength-toughness design of EBWed joints of super thick Ti6331 titanium alloy.