The microstructure and mechanical properties of molybdenum-titanium-zirconium alloy joints papered by electron beam welding with and without zirconium filler metal were evaluated. The distribution of precipitates was identified by transmission electron microscope. The stress concentration was confirmed by electron back scatter diffraction analysis and stress state was further confirmed by nanohardness test. In the weld zone of the joint without zirconium addition, Mo/Ti-dioxides were prone to segregate at grain boundaries of the weld zone, resulting in tensile stress concentration at grain boundaries. When zirconium was introduced into the weld metal, grain boundaries with segregation of Mo/Ti-dioxides would be purified by the preferential formation of ZrO2 in the grain interior in the weld zone. Tensile stress concentration was eliminated by purification of grain boundaries, leading to the enhancement of joint tensile strength. The joint welded with zirconium interlayer was fractured in a fully transgranular cleavage fracture mode, instead of a mixed fracture mode featured by the intergranular and transgranular cleavage fracture of the joint welded without zirconium addition.