SummaryIn operational modal analysis (OMA), only structural responses are typically available. In this context, bias and variance (uncertainty) errors may exist in modal estimates (especially damping estimates), resulting in inaccurate determination of the modal properties of large‐scale structures under harsh excitations. To this end, a hybrid OMA framework based on the modal decoupling, the natural excitation technique, the random decrement technique (RDT), and improved eigensystem realization algorithm (ERA) with the automated stabilization diagram is presented to perform high‐accuracy modal estimates with uncertainty quantification for large‐scale structures under normal and severe ambient excitations. The accuracy and effectiveness of the hybrid framework for identifying the modal parameters are validated by numerical simulation study of a framework structural model. Furthermore, the hybrid framework is applied to analyze recorded acceleration responses of a supertall building with 600‐m height under normal excitations and typhoon condition to verify its applicability in field measurements. The numerical simulation and field measurement studies demonstrate that the hybrid framework can not only perform precise modal estimations with uncertainty quantification through a single ambient vibration measurement but also effectively reveal the variations of modal properties of supertall structures under harsh excitations from multiple perspectives. This paper aims to enhance the reliability and accuracy of modal estimation for engineering structures and further provide insight into the variations of dynamic properties of large‐scale civil structures under severe excitations.