Friction stir welding (FSW) tool pin, as a critical component of FSW tool, plays an important role in determining the final joint properties by affecting the heat generation, plastic material flow, welding loads and so on. However, the influence of tool pin on heat and mass transfer in FSW are not elucidated. In the present study, a validated model was adopted to quantitatively analyze the effects of pin size and taper angle on the thermal process and plastic material flow in FSW. It reveals that the torque and transverse force imposed on the pin are increased with the increase of the pin diameters (including its root diameter, its tip diameter and its size in condition of constant taper angle), while the total tool torque various a little for the tool pin diameter considered in this study. When the pin diameters increase, the viscosity of the materials near the pin is decreased, while the temperature as well as the flow velocity is increased. More plastic material near the tool could rotate around the tool with an increase of the pin diameter. The TMAZ boundary is enlarged with larger pin diameters in FSW. Particularly, the shear layer thickness of the same horizontal plane in the range of 1 mm < z < 5 mm is significantly enlarged with an increase of pin root diameters. However, the shear layer thickness of the same horizontal plane in the region of z < 5 mm is increased when using a larger pin tip diameter. In addition, maximum width of TMAZ boundary at the top surface of workpiece was not affected by pin diameters. The model is validated by experimental results. It lays solid foundation for optimizing the tool pin size and taper angle in FSW.