This paper investigates the dynamic characteristics (natural frequencies and damping ratios) of a 600-m-tall supertall building with an active tuned mass damper (ATMD) system during Super Typhoon Saola. Based on the wind speed, wind direction, and wind-induced acceleration response records by the structural health monitoring (SHM) system installed on the skyscraper, the wind characteristics during the passage of Saola are first investigated, and the relations between the mean wind speeds atop the skyscraper and the root-mean-square (RMS) acceleration responses are established. Then, employing the stochastic subspace identification (SSI) method and an uncertainty quantification method, this paper comprehensively investigates the uncertainty bounds, time-varying features, and amplitude-dependency characteristics of the modal parameters with and without the operation of the ATMD system. Next, on the basis of the identified modal parameters and time-frequency analysis, the performance and effectiveness of the ATMD system in suppressing the wind-induced vibrations of the skyscraper is investigated. Lastly, the structural health condition is evaluated from the perspective of building natural frequency and damping ratio changes before and after the typhoon hit. The goal of this study is to advance the understanding of the wind effects on supertall buildings and provide useful information for the wind-resistant design and vibration control of supertall buildings in tropical cyclone-prone regions.