In the entire life cycle of a wind turbine, the probability distribution of long-term wind speeds introduces randomness to the dynamic load on the wind turbine gearbox transmission system appear random, thereby affecting the accuracy of fatigue damage prediction. In this paper, a fatigue damage prediction method is proposed for the wind turbine gearbox transmission system with considering the characteristics of the long-term wind speed probability distribution. The approach involves assessing the short-term fatigue damage of gears in the transmission system of wind turbine gearbox based on an OpenFAST-SIMPACK combined simulation model built for high power offshore wind turbines. Subsequently, surrogate model technology is used to reconstruct the mapping relationship between “average wind speed, turbulence intensity, and short-term fatigue damage” enabling the prediction of long-term fatigue damage for the gears. The research results show that the low-speed sun gear in the wind turbine gearbox transmission system is prone to contact fatigue failure. Below the rated wind speed, the short-term fatigue damage of the low-speed sun gear correlates positively with the average wind speed, thereby increasing the uncertainty of long-term fatigue damage and elevating the risk of fatigue failure.