The purpose of this study was to evaluate the temperature fluctuation induced by electromagnetic stirring (EMS) and to investigate the influence of temperature fluctuation on the appearance and microstructure of the stainless steel welds. CF8A and 308L were used for the base metal and weld metal, respectively. Bead-on-plate welding (BOP) was conducted with a linear welding machine of gas tungsten arc welding (GTAW) with EMS. The experimental results show that EMS could prompt temperature alteration rates (TARs) to fluctuate between positive and negative, and enlarge the max/min ratios. Smaller ripples and surface roughness would be induced on the welds, while the dilution and the depth-to-width ratios both decreased. As a result, the ferritic and austenitic grains become more isotropic and their grain sizes become smaller.