This article aims to present a new type of friction stir weld spindle system with 2 degrees of freedom. It explains the thermal-mechanical coupling mechanism between the welding tool and the workpiece, presents simulation of the heat distribution on a friction stir weld spindle under specific welding technology parameters, and provides the type selection and the reference design for temperature-sensitive components such as bearings and motor. The spindle system, which has high stiffness and excellent resistance to overload, is developed in accordance with the welding requirement for aluminum alloy products in the aeronautic and astronautic fields. The thermal-mechanical coupling model is established between the stir-pin and the workpiece. The heat generation and transfer processes are simulated, and the results of the temperature field distribution for the target position inside the spindle structure are obtained and verified by experiments. Test results show that the spindle system can meet the requirements of friction stir welding for large-scale complex surface structures. Simulation analysis has good consistency with experimental results, as proved by experimental verification. The resulting data can provide reliable reference design and type selection of temperature-sensitive components. Compared with other stir welding heads, this system has high stiffness and overload capacity, which can well meet the high-quality welding requirements of large-scale complex surface structures. Besides that, the thermal analytical method has universal applicability and can provide solutions for temperature field distribution of spindle under different workpiece materials and welding parameters. The friction stir weld spindle system is a novel design for welding large-scale complex surface structures. Its major advantages are the high stiffness and overload capacity. In addition, the heat and thermal simulation method, consisting of two stages, has provided the type-selection reference for the spindle design.