Ancient masonry pagodas hold significant scientific, historical, and cultural importance. However, due to the complexity of masonry materials, structures, and boundary conditions, establishing finite element static and dynamic models for ancient masonry pagodas is highly challenging. This study aimed to explore the dynamic characteristics and finite element numerical simulation methods of ancient masonry pagodas in Yongzhou, Hunan province. It focused on the Huilong Pagoda in Yongzhou, where in situ test experiments under natural excitation are conducted. The SSI and NExT-ERA methods were employed to determine the ancient pagoda’s natural frequencies, vibration patterns, and damping ratios, and to validate the NExT-ERA method. The macroscopic numerical model of the Huilong Pagoda was calibrated using measured results. Subsequently, the NExT-ERA identification results were compared and analyzed with the numerical simulation results of the dynamic characteristics. The results indicate that the first three orders of natural frequencies for the ancient pagoda in the east–west direction are 1.937 Hz, 6.802 Hz, and 21.361 Hz, respectively. Similarly, the first three orders of natural frequencies in the north–south direction are 1.935 Hz, 7.439 Hz, and 21.398 Hz. The results obtained from both methods revealed that the overall structural damping ratio ranges from 0.21% to 2.89%. The numerical model was analyzed using ANSYS, and the first three orders of natural frequencies obtained were highly consistent with the measured values, exhibiting a maximum relative error of 8.54%. The numerical simulation method developed in this study can effectively simulate masonry pagodas.