As the central component in friction stir welding, the design and manufacture of welding tools for aluminum alloys have garnered substantial attention. However, the understanding of tool reliability during the welding process, especially in terms of fatigue performance, remains unclear. This paper focuses on the welding of AA2219-T4 as a case study to elucidate the predominant failure mode of the tool during the friction stir welding (FSW) of aluminum alloys. Experimental methods, including FSW welding and fracture morphology analysis of the failed tool, coupled with numerical simulation, confirm that high-cycle mechanical fatigue fracture is the primary mode of the tool failure. Failures predominantly occur at the tool pin’s root and the shoulder end face with scroll concave grooves. The experimental and simulation results exhibit a noteworthy agreement, validating the reliability of the simulation model. The FSW Arbitrary Lagrangian–Eulerian (ALE) model developed in this study analyzes stress distribution and variation under the thermo-mechanical coupling effect of the tool. It reveals that stress concentration resulting from structural changes in the tool is the primary driver of fatigue crack initiation. This is attributed to exposure to alternating cyclic stresses such as bending, tension, and torsion at the tool pin’s root, manifesting as multiaxial composite mechanical fatigue. Among these stresses, bending alternating cyclic stress exerts the most significant influence. The paper employs the Tool Life module in DEFORM software to predict the fatigue life of the tool. Results indicate that reducing welding speed or increasing rotation speed can enhance the tool’s fatigue life to some extent. The methodology proposed in this paper serves as a valuable reference for optimizing FSW structures or processes to enhance the fatigue performance of welding tools.