Offshore floating wind turbines (FWTs) in deep water experience cyclic loadings from both environment and mechanical operations. For FWTs, the upper turbine and tower are mainly subjected to wind loading; and the floater is subjected to wave forces. It has been widely accepted that there is a strong coupling between the floater motions and the turbine forces. As the tower is placed between the upper wind turbine and the floater, both wind and wave loadings affect the cyclic forces on the tower. The construction of towers makes use of prefabricated segments. These prefabricated segments are bolted together with flanges at either end. The paper aims to investigate the axial hotspot stress on FWT’s tower base and analyze its induced fatigue damage at the welding joints around the flanges. A coupled aero-hydro-servo-elastic analysis is conducted to simulate the motion of FWTs. Then, the local welding joint along the reverse-balanced flange connection is modeled to consider the influence of local geometry. At last, the hourly fatigue damages at four locations over the tower base section are compared.