Al 1050 and Al 6061 plates with the same thickness were configured one after the other along the welding path. During friction stir welding, the rotating tool traversed from one to the other and stopped at locations with various welding distances from the initial interface. The first material was thus taken into the second material by the rotating tool as marker. A hollow inverted truncated cone-shaped rotation flow zone was confirmed, mainly occurring in shoulder-affected zone. The material in the rotation flow zone travelled with the tool and evolved upwards slowly, depositing in the weld upper part finally. EBSD investigation of the inner microstructure revealed that the strain rate at the edge of the rotation flow zone and close to the tool surface is higher than that in the mid-layer.