A novel Fe/Cu interface with excellent mechanical properties in a magnetic yoke was fabricated by friction stir welding. This method eliminated defects that commonly form during conventional bead welding. The thick oxidisation layer at the Cu/Fe surface that formed due to fusion welding was eliminated during friction stir welding (FSW). Combined with the severe deformation introduced by FSW, the Cu/Fe interface obtained by fusion welding was hardly distinguishable due to mutual embedding at the Cu/Fe interface. The in situ digital image correlation analysis indicated that this Cu/Fe interface reconstruction also modified the deformation and crack propagation behaviours. The tensile load and displacement of the joint by FSW were remarkably improved while maintaining magnetic isolation.