To address the issue of low accuracy in the dynamic modal decomposition (DMD) method used for operational modal analysis (OMA) under noise conditions of aerospace structures, an enhanced identification approach is proposed in this paper, which integrates subspace orthogonal projection with DMD to better determine the modal properties of linear mechanical systems with noisy observations. Subspace orthogonal projection applied to the Hankelized matrix is utilized for denoising observation signals. Compact singular value decomposition (SVD) is employed on the projection matrix in order to acquire the optimal realization of system matrix. Subsequently, DMD is introduced to reduce the dimensionality of the system matrix and extract the dominant modal features. The effectiveness and practicality of the proposed method are confirmed through numerical and experimental examples. The proposed method demonstrates marginally improved identification accuracy in modal frequency and enhanced performance in damping ratios when compared to representative OMA methods under different white noise conditions.