Insufficient metallurgical compatibility between Zr and Ni can lead to the formation of brittle welds and introduce thermal stress-related challenges during the electron beam welding process. Through the implementation of beam deflection and vibration, a transformation was achieved in the primary Ni₅Zr dendrite structure, transitioning from a mass into a layered configuration, consequently resulting in the formation of an ultrafine-grained eutectic−dendrite complex structure. It is revealed that the enhanced strength−ductility synergy of this structure significantly contributes to the high tensile strength and improved plasticity observed in the welded joints. As a result, the welding cracks are effectively mitigated, and notable advancements are achieved in the mechanical properties of Zr/Ni joints, elevating the tensile strength of the joints from 36.4 to 189 MPa. This research not only highlights the potential of this technique in enhancing the strength and ductility of Zr/Ni welded joints but also serves as a valuable reference for future investigations involving welding applications of dissimilar metals.