The flow pattern of materials is closely related to the formation of joint structure, has a crucial influence on the mechanical properties of joints for friction stir welding. The material flow of the joint was studied by slicing method which was adopted to observe different layer for dissimilar friction stir butt welding. The visualization of the flow material was accomplished by 3D reconstruction of the joint, which shows the flow pattern of the joint and the cause of the defect. The three-dimensional mathematical model of the flow of Al/Mg materials in FSW process is established based on computational fluid dynamics (CFD) and multiphase flow theory in this paper. The material flow patterns are analysed and predicted under different welding parameters by the distribution of tracing particles added in numerical models. The study reveals that the flow of material in the upper part of the joint is strong, the material moves to the front of tool as a whole. The magnesium alloy of the middle part in the advancing side of the joint moves forward to the front of the tool, and the temporarily cavity is filled with aluminum alloy from the retreating side. The cavity which is not completely filled will form a hole defect when the material flow is not enough due to improper process parameters. The whole joint material is mainly laminar flow. The flow mode of joint material basically does not change when the heat input is satisfied. The transfer distance and mixing mode of material will change under the condition of high rotation speed or overheat. The two materials cross the butt line for many times in mode of laminar flow around the tool and mix fully when the turbulence occurs at the retreating side.