Modal parameter identification via ambient vibration is popular but faces challenges from uncertainties due to unknown inputs and low signal‐to‐noise ratio. Bayesian methods are gaining increasing attention for operational modal identification due to their ability to quantify uncertainties. However, improvements in computational efficiency are needed, particularly when addressing numerous modes and degrees of freedom. To address this challenge, this study proposes an innovative approach, termed the “Bayesian spectral decomposition” method (BSD), employing the decompose‐and‐conquer strategy. This novel method, operating within the frequency domain, identifies each mode individually by exploiting their inherent separated modal characteristics. For each mode, the response spectrum matrix undergoes an eigenvalue decomposition, yielding crucial eigenvalues (incorporating frequency and damping information) and eigenvectors (containing mode shape information). Subsequently, statistical properties of the eigenvalues and eigenvectors are utilized to establish likelihood functions for Bayesian parameter identification. By combining prior information, the posterior probability distribution functions of modal parameters are derived. The optimal solution is then obtained by resolving the maximum posterior probability distribution function problem. To further quantify the uncertainty of modal parameters, Gaussian distributions are employed to approximate the posterior probability distribution functions. The adoption of the decomposition approach circumvents the joint identification of all modal parameters, substantially reducing the parameter dimensions for optimization. Consequently, this strategy leads to decreased computational complexity and significantly improved computational stability. The effectiveness of the BSD is confirmed through simulated data generated from an 8‐story shear building as well as measured data collected from both an experimental shear frame and the Canton Tower. The results demonstrate that the proposed method achieves high accuracy in identifying modal parameters, greatly improves computational efficiency, and effectively quantifies the uncertainties in modal parameters.