A three-dimensional transient computational fluid dynamics model is developed to analyze the influence of tool thread pitch on the material flow and thermal process in friction stir welding (FSW) of aluminum alloy plates. Four tool designs with different thread pitch are considered, the information of material flow velocity in the shear layer is extracted by analyzing the distribution of the tracking particles which are released at the starting points of streamlines, and the effect of thread pitch on material flow velocity is examined. Pin thread can effectively prevent the speed sudden change at advancing side, which is easy to occur with unthreaded pin. The total heat generation decreases with increase in thread pitch, which results in the decrease in peak temperature in FSW process. The calculated and measured thermal cycles and thermo-mechanically affected zone boundary match with each other.