The invention discloses a vacuum electron beam welding method for refractory alloy. The vacuum electron beam welding method for refractory alloy specifically comprises the steps of treatment of a weld face, preparation before welding, assembling, electron beam welding, and quality checking after welding. The vacuum electron beam welding method for refractory alloy has the characteristics that a vacuum electron beam welding environment is utilized, the penetrability is high, energy is centralized, and heat input is small; Nb521 niobium alloy with the thickness being 12 mm can be welded, and the welding performance is stable. Formation of a weld joint after welding is good, defects including cracks, air holes, pits, undercuts, weld lumps and the like of the surface of the weld joint are avoided, the internal welding quality is good, all normal-temperature mechanical properties can meet the national military standard requirements, and the high-temperature performance is good.