Summary High‐frequency force balance test is a major technical means to evaluate the wind effect of super high‐rise buildings. Most super high‐rise buildings have the characteristic that the first two‐order modal frequencies are close, and thus, considerable modal coupling effects (MCEs) may occur under wind load. For a balance model system (BMS), MCEs increase the difficulty of correcting aerodynamic distortion signals. For the wind‐induced vibration analysis of a structural system (PSS), the calculation results of the wind‐induced response and the equivalent static wind load (ESWL) may be significantly affected without considering MCE. Based on the above‐mentioned signal distortion of BMS and the modal coupling problem of PSS, this study proposes a wind‐induced vibration calculation method for the two coupled systems (BMS and PSS). The method uses the second‐order blind identification technique based on complex modal theory and the Bayesian spectral density method considering full aerodynamic characteristics to achieve effective correction of the distortion signal in BMS. In addition, it deduces the calculation method of the wind‐induced response and ESWL considering the three‐dimensional coupled vibration of a super high‐rise building. The wind effect calculation results of a 528‐m super high‐rise building confirm the necessity and effectiveness of the proposed method.