The growing demand for sustainable and affordable energy sources has led to rapid development in wind energy systems. Ensuring the long-term performance and reliability of wind turbines requires accurate estimation of fatigue damage under diverse environmental conditions. By incorporating probabilistic methods, this paper presents a comprehensive framework for long-term fatigue damage evaluation for wind turbines with high accuracy and efficiency. The proposed framework adopts the multivariate kernel density estimation to construct the high-dimensional joint probability distribution of environmental variables. A hidden Markov model serves as the driver to build the connection between historical records and future events. The short-term fatigue damage is estimated by the deep neural network based on future environmental parameters. The long-term fatigue damage is then achieved by accumulating the short-term fatigue damage evaluations with sufficient event instances. To demonstrate the applicability and effectiveness of the proposed framework, a case study is conducted with a wind turbine in the North Sea region. The fatigue damage analysis results highlight the necessity of regular inspections and maintenance for wind turbines to ensure their long-term service life and optimal performance. The framework is capable of considering a wide range of environmental factors and accounting for the inherent uncertainties and stochastic nature, providing a robust and comprehensive approach for estimating fatigue damage of wind turbines as well as other structures under long-term environmental conditions.