Narrow gap multi-layer hybrid welding technology is an efficient way to join thick plates of metal or alloys. However, the coarse microstructure and solute segregation were caused by rapid cooling. In this paper, a magnetic field was utilized to achieve better microstructural control during welding. Using analytical electron microscopy combining with EDS and EBSD, microstructure evolution including grain growth and solute segregation during electromagnetic stirring (EMS) was systematically studied. EMS promoted the refinement and suppressed the overgrowth of austenite (γ) grains. Besides, γ exhibited equiaxed grains as seen from both grain size and texture evolution. For ferrite (δ) dendrites, EMS promoted the morphological transition from the coarse and long vermicular morphology to the fine lathy forms. EMS also induced deviation and discontinuity in δ dendrite growth. From chemical compositions point-of-view, a homogeneous distribution was obtained at both macro- and micro-scales by EMS. These results were attributed to δ “dendrite fragmentation” behavior brought by electromagnetic force at solid/liquid interface. Such δ fragments grew and acted as a substrate for epitaxial γ grains nucleation, with specific γ/δ orientation relationships, suppressing continuous epitaxial growth of γ grains via increased nucleation. Moreover, δ fragments result in reduced fraction of δ phase and dispersed distribution.