Abstract: The coupled governing equation of motion of the offshore wind turbine（OWT）substructure with pile foundation flexibilities is established based on the fully coupled analysis theories of the numerical simulation tool FAST and the linearized theories of pile-soil interactions. Then the coupled numerical model of the rotor nacelle assembly,tower and substructure with the flexible boundary conditions（coupled springs）under earthquake,wind and wave loads is established in the updated FAST v8. Based on the established coupled numerical model,the dynamic responses of OWT under the combined actions of earthquake,wind and wave loads are investigated,and the variations of the structural dynamics and coupling mechanisms owing to the pile foundation flexibilities is highlighted. The results prove the significant influence of the pile foundation flexibilities on the structural dynamic characteristics of OWT. The influence of the second modes on the tower top displacements shall be impaired,while with the overestimated contributions of the high order modes on the bending moments at the mudline,if the pile foundation flexibilities are neglected in the seismic analysis of OWT. Sequentially,the remarkable discrepancies of the OWT seismic responses are observed. Hence,the pile foundation flexibilities should be considered in the design and research of OWTs under earthquakes.