The accuracy of identifying dynamic characteristics of super-tall buildings under typhoon conditions, as well as their correlation with the vibration amplitude, remains unclear, limiting the effective assessment of the structural performance and optimization of wind-resistant designs. To address this issue, the measured wind-generated vibration responses of Shanghai World Finance Center during the passage of Typhoon “Rumbia” were derived using data obtained from the health monitoring system of a super-tall building in Shanghai. The first and second inherent frequencies, as well as the damping ratio of the structure, were ascertained through the employment of the curve method and the standard deviation method. Based on this, a comparison and analysis were carried out regarding the variation patterns of the first and second inherent frequencies and the damping ratio with reference to the vibration amplitude. Vibration modes were identified using frequency domain analysis. The results of the natural frequency identification were compared to those from the Peak Picking method to see how well the curve method and the standard deviation method worked at finding modal parameters. Ultimately, an assessment of the super-tall building’s performance during the impact of the typhoon was conducted. The results demonstrate that the curve method and the standard deviation method can accurately identify the inherent frequency and damping ratio of the structure, with the curve method revealing a more pronounced regularity of the modal parameters. For the structure, in the horizontal and longitudinal directions, the first and second inherent frequencies exhibit a negative correlation with amplitude, while the damping ratio shows a positive correlation with amplitude. Moreover, as the floor level rises, the vibration modes in both directions of the structure steadily increase. During the impact of Typhoon “Rumbia”, the building’s performance complied with the requirements set by comfort standards. These analytical results not only provide valuable references for the wind-resistant design and vibration control of super-tall buildings but also offer critical support for condition assessment and damage identification within structural health monitoring systems.