In this paper, the non-uniform microstructure and high temperature coordinated deformation behavior of 2A97 / 5A06 dissimilar aluminum alloy friction stir welded plate were studied. The microstructure of each area of the welded joint was observed, and the high temperature mechanical properties of each area and the whole joint was studied. It was found that the grains in the weld nugget zone of 2A97 and 5A06 were fine. The grain size of each region on the 2A97 side was small and basically close, and the grain size of each region on the 5A06 side was slightly larger and the difference was obvious. Under the process parameter of 430 °C and 10_-3 s_-1^{, the} high temperature properties of 2A97 and 5A06 base metals are better, and the elongations are 278.8 % and 118.6 %, respectively. The strength and elongation of the nugget zone of the joint are 18.4 MPa and 176.1 %, respectively, which are between 2A97 and 5A06. The strength is about 2 times that of the 2A97 base metal, and the elongation is about 1.5 times that of the 5A06 base metal. The overall performance shows an obvious superposition principle. The deformation resistance of each region is different. The vertical weld specimen fractured after concentrated deformation in the 2A97 thermo-mechanically affected zone. After correction, the flow stress was slightly higher than that of the base metal and the elongation was close to that of the base metal. The grain size and flow stress of each region after welding meet the creep equation. The smaller the grain size, the lower the flow stress.