In this study, a 3D coupled thermo-mechanical finite element model is developed to predict and analyze the defect formation during friction stir welding based on coupled Eulerian Lagrangian method. The model is validated by comparing the estimated welding temperature, processed zone shape and void size with those obtained experimentally. The results compared indicate that the simulated temperature and the data measured are in good agreement with each other. In addition, the model can predict the plasticized zone shape and the presence of a void in the weld quite accurately. However, the void size is overestimated. The effects of welding parameters and tool pin profile are also analyzed. The results reveal that welding at low welding speed or high tool rotational speed could produce a smaller void. Moreover, compared to a smooth tool pin, a featured tool pin can enhance plastic flow in the weld and achieve defect-free weldment. The results are helpful for the optimization of the welding process and the design of welding tools.