Modal parameters are used as safety assessment indicators for evaluating the structural integrity of buildings in various ways. In particular, the modal damping ratio plays a crucial role in accurately predicting the serviceability and safety of buildings, starting from the initial design stage. However, the identification results of the modal damping ratio can become unstable due to measurement time, initial configuration conditions used in the analysis, and nonstationary responses included in the structural response. To address the instability issue, this study proposes a long short-term memory-based frequency domain decomposition (FDD-LSTM) method. The FDD-LSTM method utilizes the acceleration response of the building as input data and the modal damping ratio obtained from the FDD method as output data, constructing an LSTM network model for the relationship between the acceleration response and modal damping ratio. The FDD-LSTM method exhibited a discrepancy of less than 0.02% compared to the reference value of the modal damping ratio obtained through free vibration response. Furthermore, when applied to data acquired from an actual building, the method demonstrated a variance of approximately 5%. The proposed FDD-LSTM method is validated for stability performance using a three-degree-of-freedom numerical analysis model, a 3-story steel frame structure model, and a 117-story high-rise building. The FDD-LSTM method, trained on a large dataset, enables generalized estimation and addresses instability issues related to modal damping ratio.