During the friction stir welding (FSW), the property of the welding joint is highly affected by the plastic and viscous flow behavior of the softened material. The flow pattern of the welded material was examined through observing the microstructural distribution of friction stir welded joints between dissimilar 2024 and 1060 aluminum alloy. The experimental results show that the flow patterns of material at different locations in the weld are different and can be divided into four layers along the thickness direction: surface flow layer influenced by the shoulder of the tool, in which the material tends to flow as integrity; horizontal flow layer influenced by the surface flow layer, in which the material of surface flow layer enters and flows forwards under the advancing force of the tool; vertical flow layer (plastic flow area induced by stirring of the pin), in which the flow pattern is complex and onion rings can often be observed; unstirred bottom layer because of the length of the pin being shorter than the thickness of the plates. The effect of plastic flow on welding quality was further investigated. The study suggests that welding quantity is significantly influenced by the flow pattern and defects always appear in horizontally lamellar flow region because of the complex flow pattern.