Vibration-based damage assessment technology is a hot topic in aerospace engineering, civil engineering, and mechanical engineering. In this paper, a damage assessment approach using multiple-stage dynamic flexibility analysis is proposed for structural safety monitoring. The proposed method consists of three stages. The content of Stage I is to determine the number of damaged elements in the structure by the rank of dynamic flexibility change. The content of Stage II is to determine damage locations by the minimum rank of flexibility correlation matrices. Finally, the damage extents of those damaged elements are calculated in Stage III. The proposed approach fully uses the filtering ability of matrix rank analysis for data noise. A 27-bar truss structure and a steel frame structure are used as the numerical and experimental examples to demonstrate the proposed method, respectively. From the numerical and experimental results, it is found that structure damages can be successfully identified through the multiple-stage dynamic flexibility analysis. By comparative study, the proposed method has more powerful antinoise ability and higher calculation accuracy than the generalized flexibility method. The proposed method may be a promising tool for structural damage assessment.