Abstract: Many offshore wind farms in China are situated in seismically active regions. Under seismic loading, pile–soil interaction can lead to reduced foundation stiffness and shifts in natural frequencies, which may induce structural resonance and fatigue damage. Accurate prediction of the natural frequencies of monopile foundations and assessment of their structural seismic performance are therefore essential for ensuring the long-term operational safety of wind turbines. This study focuses on monopile foundations for offshore wind turbines. By combining numerical simulation with theoretical analysis, the evolution mechanism of natural frequencies and the influence of various parameters were systematically investigated. Based on the Boulanger foundation model, which accounts for pile–soil interaction, a simplified numerical model of the monopile foundation was developed in OpenSees. A comprehensive sensitivity analysis was conducted to examine the influence of soil and pile parameters on the natural frequencies of both long and short piles in sand and clay. Furthermore, by considering four stratified soil scenarios— “sand over clay”, “clay over sand”, “sand-clay-sand” and “clay-sand-clay”— how the sequence of soil layers affects parameter sensitivity was explored. This study provides a theoretical foundation for predicting the dynamic behavior and guiding the seismic design of monopile foundations for offshore wind turbines in seismic regions, offering valuable insights for improving the seismic safety and resilience of wind turbine structures.