As the lightest engineering materials, magnesium alloys have been widely used. Because of the specific chemical and physical characteristics, the weldability of magnesium alloy is poor. Adopting suitable welding technology and improving the quality of magnesium alloy welded joints is key to their successful application. According to previous research data, it was found that the combined action of magnetic field and activated flux has a positive effect on improving-welding efficiency and improving the properties of a welded joint, butanalysis of microstructure evolution is insufficient. In this paper, AZ91 magnesium alloy was welded by TIG welding with activated flux and external longitudinal AC magnetic field. The phase composition and microstructure evolution were investigated. The experimental results revealed that the phase composition of welded joint was not changed due to the introduction of the magnetic field and activated flux, the growth patterns of grain in the weld seam and heat-affected zone were different. When the activated flux amount was 3 mg/cm2 with the effect of the magnetic field, the grain size of the weld seam was the finest, which was 18.96 μm. However, the grain size of the weld seam was larger than that of base metal. The crystallographic characteristics of grain boundaries in the weld seam and base metal were both LAGBs. The microstructure of the weld seam was messier than the base metal due to the larger misorientation angle. Under the combined action of the magnetic field and activated flux, the crystallization nucleation condition of the molten pool was changed, the formation of twins was promoted, and the crystal could selectively grow parallel with the (0001) basal plane.