Abstract: The modified suction caisson incorporates a larger-diameter, shorter external structure at the top of the regular suction caisson, enhanced bearing capacity and displacement control ability. The natural frequency of the modified suction caisson varies under long-term cyclic loading in operation. Resonance occurs when the natural frequency coincides with the environmental load frequency. Model tests and numerical simulations were conducted to investigate the effects of cyclic load amplitude, frequency, and loading pattern on the natural frequency of modified suction caissons. The variation of natural frequency under various foundation model scales was analyzed. The results indicate that under cyclic loading, the natural frequency of modified suction caissons initially increases and subsequently decreases as the number of cycles increases. Compared with the regular suction caisson, the peak natural frequency value of the modified suction caisson decreases by 0.44%, 1.36%, and 7.5%, respectively. The peak and final values of natural frequency gradually increase with increasing cyclic load amplitude and frequency. Unidirectional cyclic loading produces the maximum peak natural frequency, followed by bidirectional symmetric cyclic loading, and bidirectional asymmetric cyclic loading yields the minimum. Under long-term cyclic loading, the variation of natural frequency in modified suction caissons is smaller than that in regular suction caissons. Model tests were performed on suction caissons of different materials (steel, aluminum, and polypropylene). Polypropylene was identified as the optimal material for studying natural frequency variation patterns of suction caissons under 1-g model test conditions. The peak and final values of natural frequency of modified suction caissons exhibit a linear increase with scale. The research findings provide theoretical references for the natural frequency design of modified suction caissons in offshore wind power engineering applications.