The thermal modeling of underwater friction stir welding (FSW) was conddcted with a three-dimensional heat transfer model. The vaporizing characteristics of water were analyzed to illuminate the boundary conditions of underwater FSW. Temperature dependent properties of the material were considered for the modeling. FSW experiments were carried out to validate the calculated results, and the calculated results showed good agreement with the experimental results. The results indicate that the maximum peak temperature of underwater joint is significantly lower than that of normal joint, although the surface heat flux of shoulder during the underwater FSW is higher than that during normal FSW. For underwater joint, the high-temperature distributing area is dramatically narrowed and the welding thermal cycles in different zones are effectively controlled in contrast to the normal joint.